Classifications

• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
  • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
  • C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
  • C07K14/47—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P1/00—Drugs for disorders of the alimentary tract or the digestive system
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P11/00—Drugs for disorders of the respiratory system
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P11/00—Drugs for disorders of the respiratory system
  • A61P11/06—Antiasthmatics
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P13/00—Drugs for disorders of the urinary system
  • A61P13/12—Drugs for disorders of the urinary system of the kidneys
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P15/00—Drugs for genital or sexual disorders; Contraceptives
  • A61P15/18—Feminine contraceptives
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P17/00—Drugs for dermatological disorders
  • A61P17/06—Antipsoriatics
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P19/00—Drugs for skeletal disorders
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P19/00—Drugs for skeletal disorders
  • A61P19/02—Drugs for skeletal disorders for joint disorders, e.g. arthritis, arthrosis
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P19/00—Drugs for skeletal disorders
  • A61P19/08—Drugs for skeletal disorders for bone diseases, e.g. rachitism, Paget's disease
  • A61P19/10—Drugs for skeletal disorders for bone diseases, e.g. rachitism, Paget's disease for osteoporosis
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P21/00—Drugs for disorders of the muscular or neuromuscular system
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P25/00—Drugs for disorders of the nervous system
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P25/00—Drugs for disorders of the nervous system
  • A61P25/28—Drugs for disorders of the nervous system for treating neurodegenerative disorders of the central nervous system, e.g. nootropic agents, cognition enhancers, drugs for treating Alzheimer's disease or other forms of dementia
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P29/00—Non-central analgesic, antipyretic or antiinflammatory agents, e.g. antirheumatic agents; Non-steroidal antiinflammatory drugs [NSAID]
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P3/00—Drugs for disorders of the metabolism
  • A61P3/04—Anorexiants; Antiobesity agents
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P3/00—Drugs for disorders of the metabolism
  • A61P3/08—Drugs for disorders of the metabolism for glucose homeostasis
  • A61P3/10—Drugs for disorders of the metabolism for glucose homeostasis for hyperglycaemia, e.g. antidiabetics
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
  • A61P31/04—Antibacterial agents
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
  • A61P31/10—Antimycotics
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
  • A61P31/12—Antivirals
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
  • A61P31/12—Antivirals
  • A61P31/14—Antivirals for RNA viruses
  • A61P31/18—Antivirals for RNA viruses for HIV
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P33/00—Antiparasitic agents
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P35/00—Antineoplastic agents
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P35/00—Antineoplastic agents
  • A61P35/02—Antineoplastic agents specific for leukemia
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P37/00—Drugs for immunological or allergic disorders
  • A61P37/02—Immunomodulators
  • A61P37/06—Immunosuppressants, e.g. drugs for graft rejection
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P37/00—Drugs for immunological or allergic disorders
  • A61P37/08—Antiallergic agents
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P7/00—Drugs for disorders of the blood or the extracellular fluid
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P7/00—Drugs for disorders of the blood or the extracellular fluid
  • A61P7/02—Antithrombotic agents; Anticoagulants; Platelet aggregation inhibitors
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P7/00—Drugs for disorders of the blood or the extracellular fluid
  • A61P7/10—Antioedematous agents; Diuretics
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P9/00—Drugs for disorders of the cardiovascular system
  • A61P9/10—Drugs for disorders of the cardiovascular system for treating ischaemic or atherosclerotic diseases, e.g. antianginal drugs, coronary vasodilators, drugs for myocardial infarction, retinopathy, cerebrovascula insufficiency, renal arteriosclerosis
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P9/00—Drugs for disorders of the cardiovascular system
  • A61P9/12—Antihypertensives
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K38/00—Medicinal preparations containing peptides
• • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
  • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
  • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
  • Y02A90/00—Technologies having an indirect contribution to adaptation to climate change
  • Y02A90/10—Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation
• • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
  • Y10—TECHNICAL SUBJECTS COVERED BY FORMER USPC
  • Y10T—TECHNICAL SUBJECTS COVERED BY FORMER US CLASSIFICATION
  • Y10T436/00—Chemistry: analytical and immunological testing
  • Y10T436/14—Heterocyclic carbon compound [i.e., O, S, N, Se, Te, as only ring hetero atom]
  • Y10T436/142222—Hetero-O [e.g., ascorbic acid, etc.]
  • Y10T436/143333—Saccharide [e.g., DNA, etc.]

Definitions

• This invention relates to a new family of proteins, termed the SECFAM3 family, its family members including the novel proteins INSP123, INSP124 and INSP125, herein identified as secreted proteins containing a von Willebrand Factor type C (vWFC) domain, ranging from 50 to 60 amino acids in length and containing ten conserved cysteine residues and to the use of these proteins and nucleic acid sequences from the encoding genes in the diagnosis, prevention and treatment of disease.
• vWFC von Willebrand Factor type C
• bioinformatics tools increase in potency and in accuracy, these tools are rapidly replacing the conventional techniques of biochemical characterisation. Indeed, the advanced bioinformatics tools used in identifying the present invention are now capable of outputting results in which a high degree of confidence can be placed.
• the ability of cells to make and secrete extracellular proteins is central to many biological processes. Enzymes, growth factors, extracellular matrix proteins and signalling molecules are all secreted by cells. This is through fusion of a secretory vesicle with the plasma membrane. In most cases, but not all, proteins are directed to the endoplasmic reticulum and into secretory vesicles by a signal peptide. Signal peptides are cis-acting sequences that affect the transport of polypeptide chains from the cytoplasm to a membrane bound compartment such as a secretory vesicle. Polypeptides that are targeted to the secretory vesicles are either secreted into the extracellular matrix or are retained in the plasma membrane.
• polypeptides that are retained in the plasma membrane will have one or more transmembrane domains.
• secreted proteins that play a central role in the functioning of a cell are cytokines, hormones, extracellular matrix proteins (adhesion molecules), proteases, and growth and differentiation factors.
• the von Willebrand Factor type C (vWFC) domain is characterised by a conserved spatial pattern of 10 cysteines within a region of about 56 amino acids in length. These domains are a common feature in large, extracellular, multi-domain proteins, including Chordin, Thombospondin, Type IIA procollagen and Ventroptin. They are also found in smaller proteins associated with the regulation of development, such as SOG (Short Gastrulation). vWFC domains were first characterised in the von Willebrand Factor protein. This protein was seen to be important in blood clotting at the site of vessel damage by participating in platelet-vessel endothelial cell interactions through the formation of a non-covalent complex with coagulation factor VIII at the site of the wound. In this case, vWFC domains were thought to be involved in protein oligomerization events. The fact that this domain is also found in other complex forming proteins points towards a role in protein-protein interaction during the formation of complexes.
• vWFC domains The role of vWFC domains in the developmental process has also been highlighted.
• BMPs Bone Morphogenic Proteins
• This antagonistic binding may play a regulatory role in the development of cartilage and bone during skeletal development.
• BMPs may have a role to play in conditions of excessive cartilage and bone growth, such as osteoarthritis.
• therapeutic proteins containing vWFC domains may help to control the progression of such conditions.
• a secreted protein ligand is a protein that is secreted from a particular cell and elicits a phenotypic response in the same/or another cell by modulating (including ligand-antagonism, as demonstrated by the Dan family) the activity of a cognate receptor and downstream signal transduction pathway.
• An example of an already known secreted protein ligand family is the glycoprotein hormone family.
• Follicle-stimulating hormone is a member of the glycoprotein hormone family.
• FSH is secreted by the cells of the anterior lobe of the pituitary gland, enters the bloodstream, and then binds cognate receptors on the Sertoli cells of the testes to regulate the process of spermatogenesis.
• FSH binds receptors on the thecal, stromal and granulosa cells of the ovary to regulate ovulation.
• FSH deficiencies can lead to infertility problems in both men and women. Restoring the levels of FSH by administering FSH in the form of a protein therapeutic can be used to combat FSH-triggered infertility.
• FSH is available as GONAL-fTM (Serono).
• the invention is based on the discovery that the INSP123, I SP124 and INSP125 polypeptides are secreted proteins, more specifically, vWFC-domain containing secreted proteins. Together, INSP123, L SP124 and INSP125 form part of a family of proteins herein identified as the SECFAM3 family of proteins. INSP123, INSP124 and INSP125 are predicted to be splice variants with variant functions, such as different affinities for their binding partners.
• the proteins of the present invention have no associated publicly available annotation, contain a strong secretory protein signature in the form of a signal peptide, and can be clustered with similar proteins, supported by orthologues from other animal species. Further examination has permitted the construction of a hitherto uncharacterised family of proteins comprising 2 human genes and which, including vertebrate and chordate orthologues, presently comprises 22 sequences in total. This cluster of related sequences will herein be referred to as the "SECFAM3 family.”
• a method of identifying a member of the SECFAM3 family comprising: searching a database of translated nucleic acid sequences or polypeptide sequences to identify a polypeptide sequence that matches the following sequence profile: A R N D C Q E G H II LL KK MM F P S T Y V M -2 -2 -3 -4 -2 -1 -3 -4 -3 0 0 2 2 - -22 8 8 0 -3 -2 -2 -2 -2 0 A 3 -1 -3 -3 -1 -2 -2 -3 00 00 11 22 1 -2 -1 -1 -3 -1 1 L 1 -2 -2 -3 -2 -2 -2 2 0 2 -2 0 -2 0 1 -1 -3 -2 2 H -1 -1 1 -1 -3 -1 -1 -3 -1
• a "member of the SECFAM3 family” is thus to be interpreted herein as a polypeptide sequence that satisfies the profile described above with a maximum threshold E value of IO "2 when used as a query sequence in BLAST using the parameters described above.
• the polypeptide sequence has a minimum threshold E value of 10 "5 or less, 10 "10 or less, IO "50 or less, most preferably, 10 " TM or less.
• the E value generated is e "143 .
• An E value represents the expected number of better or equally good matches found in a database at random, or alternatively may be described as the probability that a match has occurred at random.
• all hits are ranked according to their E-values, which, in turn, depend on a) the number of candidates available for each sequence position (20 in the case of amino acids), the length of the sequence or matching region, and the size of the database searched. Shorter sequences such as the members of the SECFAM3 family therefore tend to have larger E-values than a comparable match between two longer sequences.
• the above profile takes into account the existence of a signal sequence and a vWFC domain.
• the profile allows for a higher degree of variability in the amino acid sequence of the signal peptide region (amino acids 1 to 23) compared to the vWFC domain.
• "Variability" in this context relates to the degree of similarity and identity between the amino acid sequences. This reflects the situation found with the 22 members of the SECFAM3 family that are identified herein.
• the high degree of similarity shared in the vWFC-like domains between the fifteen members also suggests that the vWFC-like domain is likely to be involved in an important function of the molecule. If this domain was of less importance, the degree of conservation amongst its members would not be so high.
• the database of translated nucleic acid sequences that is searched may include, but is not limited to, translated nucleic acid sequences derived from cDNAs, ESTs, mRNAs, whole or partial genome databases.
• (ii) is a fragment thereof which is a member of the vWFC domain containing protein family, or has an antigenic determinant in common with the polypeptides of (i); or
• a polypeptide according to the invention is a member of the vWFC-domain containing secreted protein family.
• the polypeptide gives a maximum threshold E value of IO "2 .
• the polypeptide sequence has a minimum threshold E value of 10 "5 or less, 10 "10 or less, 10 "50 or less, most preferably, IO "70 or less. Lowering the threshold value acts as a more stringent filter to separate polypeptides comprising a signal peptide and vWFC domain from the general background polypeptide sequences.
• an isolated polypeptide which (i) comprises a polypeptide satisfying the consensus amino acid sequence:
• (ii) is a fragment thereof which is a member of the vWFC domain containing protein family, or has an antigenic determinant in common with the polypeptides of (i); or
• a polypeptide according to the invention is a member of the vWFC-domain containing secreted protein family.
• the sequence recited in this embodiment of the invention covers the high identity region from L SP124 (SEQ ID NO: 12) amino acid position 54-171 (amino acids 155-279 of the alignment, see figure 1).
• the polypeptide comprises or consists of a polypeptide satisfying the consensus amino acid sequence
• an isolated polypeptide which consists of a polypeptide satisfying the consensus amino acid sequence
• an isolated polypeptide of the third embodiment of the second aspect of the invention wherein the isolated polypeptide comprises one or more, preferably, all of 10 cysteine residues at amino acid positions 2, 23, 25, 27, 34, 40, 47, 57, 58 and 61 of the consensus amino acid sequence of the third to fifth embodiments of the second aspect of the invention.
• the isolated polypeptide comprises one or more, preferably, all of 10 cysteine residues at amino acid positions 68, 88, 91, 93, 101, 109, 114, 124, 125 and 128 of the consensus amino acid sequence of the fourth embodiment of the second aspect of the invention.
• the isolated polypeptide comprises one or more, preferably, all of the cysteine residues at amino acid positions 2, 23, 25, 27, 34, 40, 47, 57, 58, 61, 68, 88, 91, 93, 101, 109, 114, 124, 125 and 128 of the consensus amino acid sequence of the fourth embodiment of the second aspect of the invention.
• amino acid sequences of the third to fifth embodiments of the second aspect of the invention are written in PROSITE (protein sites and patterns) notation, with the amino acids being represented by their one-letter codes (Bairoch, A., Bucher, P., and Hofmann, K., (1997).
• PROSITE Database Its status in 1997. Nucl. Acids Res. 25, 217-221). Briefly, a peptide comprising the following formula:
• A(l)-x(il,jl)-A2-x(i2,j2)-....A ⁇ p-l ⁇ -x(i ⁇ p-l ⁇ ,j ⁇ p-l ⁇ )-Ap is to be interpreted in the following manner.
• A(k) is a component, either specifying one amino acid, e.g. C, or a set of possible amino acids, e.g. [ILVF].
• a component A(k) is an identity component if it specifies exactly one amino acid (for instance C or L) or an ambiguous component if it specifies more than one (for instance [ILVF] or [FWY]).
• the part x(ikjk) specifies a wildcard region of the pattern matching between ik and jk arbitrary amino acids.
• a wildcard region x(ikjk) is "flexible" if jk is bigger than ik (for example x(2,3).
• the flexibility of such a region is jk-ik.br>
• the flexibility of x(2,3) is 1.
• the wildcard region is fixed if j(k) is equal to i(k), e.g., x(2,2) which can be written as x(2).
• the product of flexibility for a pattern is the product of the flexibilities of the flexible wildcard regions in the pattern, if any, otherwise it is defined to be one.
• C-x(2)-H is a pattern with two components (C and H) and one fixed wildcard region. It matches any sequence containing a C followed by any two arbitrary amino acids followed by an H. Amino acid sequences ChgHyw and liChgHlyw would be included in the formula.
• C-x(2,3)-H is a pattern with two components (C and H) and one flexible wildcard region. It matches any sequence containing a C followed by any two or three arbitrary amino acids followed by an H such as aaChgHywk and liChgaHlyw.
• C-x(2,3)-[ILV] is a pattern with two components (C and [UN]) and one flexible wildcard region.
• polypeptide which: (i) comprises the amino acid sequence as recited in SEQ ID ⁇ O:2, SEQ ID NO:4, SEQ ID NO:
• (ii) is a fragment thereof which is a member of the vWFC domain containing protein family, or has an antigenic determinant in common with the polypeptides of (i); or
• polypeptide which consists of the amino acid sequence as recited in SEQ ID NO:2 SEQ ID NO:4, SEQ ID NO:39, SEQ ID NO:41 , SEQ ID NO:43 and/or SEQ ID NO:45.
• the polypeptide having the sequence recited in SEQ ID NO:2 is referred to hereafter as the 'TNSP123 polypeptide".
• the first 23 amino acids of the INSP123 polypeptide form a signal peptide.
• the INSP123 full length polypeptide sequence with and without the signal sequence are recited in SEQ ID NO: 2 and SEQ ID NO:4, respectively.
• the polypeptide having the sequence recited in SEQ ID NO:4 is referred to hereafter as "the INSP123 mature polypeptide".
• the Applicant does not wish to be bound by this theory, it is postulated that the first 22 amino acids of the INSP123 cloned polypeptide form a signal peptide.
• the INSP123 cloned full length polypeptide sequence with and without the signal sequence are recited in SEQ ID NO: 39 and SEQ ID NO:41, respectively.
• the polypeptide having the sequence recited in SEQ ID NO:39 is referred to hereafter as "the INSP123 cloned polypeptide”.
• the polypeptide having the sequence recited in SEQ ID NO:41 is referred to hereafter as "the INSP123 cloned mature polypeptide 1".
• the first 21 amino acids of the INSP123 cloned polypeptide form a signal peptide.
• the INSP123 cloned full length polypeptide sequence with and without the signal sequence are recited in SEQ ID NO: 39 and SEQ ID NO:43, respectively.
• the polypeptide having the sequence recited in SEQ ID NO:39 is referred to hereafter as "the INSP123 cloned polypeptide”.
• the polypeptide having the sequence recited in SEQ ID NO:43 is referred to hereafter as "the INSP123 cloned mature polypeptide 2".
• the first 31 amino acids of the INSP123 cloned polypeptide form a signal peptide.
• the INSP123 cloned full length polypeptide sequence with and without the signal sequence are recited in SEQ ID NO: 39 and SEQ ID NO:45, respectively.
• the polypeptide having the sequence recited in SEQ ID NO:39 is referred to hereafter as "the INSP123 cloned polypeptide”.
• the polypeptide having the sequence recited in SEQ ID NO:45 is referred to hereafter as "the INSP123 cloned mature polypeptide 3".
• the antigenic determinant, fragment or functional equivalent of the second embodiment of the third aspect of the invention comprises one or more of the ten cysteine residues at amino acid positions 53, 74, 76, 78, 85, 90, 97, 105, 106 and 107 of SEQ ID NO:2. More preferably, one or more of these cysteine residues participate in disulphide bond formation under physiological conditions, fn this aspect of the invention, by "physiological conditions" is meant the natural environment in which the native or wildtype form of the polypeptide would be found. Disulphide bond formation is often integral to the correct conformation of a protein and thus, its function. Disulphide bond formation is often integral to the correct conformation of a protein and thus, its function. It is therefore important that such cysteine residues be conserved.
• a polypeptide which:
• (i) comprises the amino acid sequence as recited in SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:
• (ii) is a fragment thereof which is a member of the vWFC domain containing protein or having an antigenic determinant in common with the polypeptides of (i); or
• polypeptide according to this third aspect of the invention consists of the amino acid sequence as recited in SEQ ID NO: 12, SEQ ID NO: 16, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51 and/or SEQ ID NO:53,
• the antigenic determinant, fragment or functional equivalent of the fourth embodiment of the third aspect of the invention comprises one or more of the ten cysteine residues at amino acid positions 53, 74, 76, 78, 85, 90, 97, 105, 106 and 109 of SEQ ID NO:12. More preferably, one or more of these cysteine residues participate in disulphide bond formation under physiological conditions. Even more preferably, said antigenic determinant, fragment or function equivalent further comprises one or more of the ten cysteine residues at amino acid positions 116, 134, 137, 139, 147, 152, 157, 167, 168 and 171.
• the polypeptide having the sequence recited in SEQ ID NO:6 is referred to hereafter as "the INSP124 exon 1 polypeptide".
• the polypeptide having the sequence recited in SEQ ID NO: 8 is referred to hereafter as "the INSP124 exon 2 polypeptide”.
• the polypeptide having the sequence recited in SEQ ID NO:10 is referred to hereafter as "the INSP124 exon 3 polypeptide”.
• the polypeptide having the sequence recited in SEQ ID NO: 12 is referred to hereafter as "the INSP 124 polypeptide”.
• INSP124 is predicted to be similar to Ventroptin, also known as Neuralin, a BMP-4 (bone mo ⁇ hogenetic protein 4) antagonist expressed in a double gradient pattern in the retina.
• BMPs are multifunctional secreted proteins which signal through specific receptors. They have a key role in chondrogenesis deduced by their ability to induce ectopic chondrogenesis in adult animals (Chimal-Monroy J et al, Dev Biol. 2003 May 15;257(2):292-301).
• Ventroptin is a member of the chordin family and known to antagonize BMP2 as well as BMP4 (Takahashi H et al, Development. 2003 Nov;130(21):5203-15). Misexpression of Ventroptin altered expression patterns of several topographic genes in the retina and projection of the retinal axons to the tectum along both axes. Thus, topographic retinotectal projection appears to be specified by the double-gradient molecule Ventroptin along the two axes (Sakuta H et al, Science. 2001 Jul 6;293(5527):111-5).
• ventroptin presents a broad expression pattern in many tissues such as dorsal root ganglia, gut, condensing cartilages of the skeleton and developing hair follicles.
• CHL2 chordin-like protein
• the first 23 amino acids of INSP124 exon 1 polypeptide form a signal peptide.
• the INSP124 exon 1 and full length polypeptide sequences without the signal sequence are recited in SEQ ID NO: 14 and SEQ ID NO: 16, respectively.
• the polypeptide having the sequence recited in SEQ ID NO: 14 is referred to hereafter as "the INSP124 exon 1 mature polypeptide”.
• the polypeptide having the sequence recited in SEQ ID NO: 16 is referred to hereafter as "the INSP124 mature polypeptide”.
• the Applicant does not wish to be bound by this theory, it is postulated that the first 22 amino acids of the INSP124 cloned polypeptide form a signal peptide.
• the INSP124 cloned full length polypeptide sequence with and without the signal sequence are recited in SEQ ID NO:47 and SEQ ID NO:49, respectively.
• the polypeptide having the sequence recited in SEQ JD NO:47 is referred to hereafter as "the I SP124 cloned polypeptide”.
• the polypeptide having the sequence recited in SEQ ID NO:49 is referred to hereafter as "the I SP124 cloned mature polypeptide 1".
• the first 21 amino acids of the INSP124 cloned polypeptide form a signal peptide.
• the INSP124 cloned full length polypeptide sequence with and without the signal sequence are recited in SEQ ID NO:47 and SEQ ID NO:51, respectively.
• the polypeptide having the sequence recited in SEQ ID NO:47 is referred to hereafter as "the INSP124 cloned polypeptide”.
• the polypeptide having the sequence recited in SEQ ID NO:51 is referred to hereafter as "the INSP124 cloned mature polypeptide 2".
• the first 31 amino acids of the MSP 124 cloned polypeptide form a signal peptide.
• the INSP124 cloned full length polypeptide sequence with and without the signal sequence are recited in SEQ JD NO:47 and SEQ JD NO:53, respectively.
• the polypeptide having the sequence recited in SEQ JD NO:47 is referred to hereafter as "the INSP124 cloned polypeptide”.
• the polypeptide having the sequence recited in SEQ JD NO:53 is referred to hereafter as "the INSP124 cloned mature polypeptide 3".
• INSP124 exon polypeptides as used herein includes polypeptides comprising the INSP124 exon 1 polypeptide, the INSP124 exon 2 polypeptide, the INSP124 exon 1 mature polypeptide, the INSP124 exon 3 polypeptide, the INSP124 polypeptide, the INSP124 mature polypeptide 1, the INSP124 mature polypeptide 2, or the INSP124 mature polypeptide 3, as well as polypeptides consisting of the JJSTSP124 exon 1 polypeptide, the INSP124 exon 1 mature polypeptide, the INSP124 exon 2 polypeptide, the INSP124 exon 3 polypeptide, the INSP124 polypeptide or the INSP124 mature polypeptide.
• (ii) is a fragment thereof which is a member of the vWFC domain containing protein or having an antigenic determinant in common with the polypeptides of (i); or
• a polypeptide which consists of the amino acid sequence as recited in SEQ ID NO: 18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ JD NO:26, SEQ ID NO:28, SEQ JD NO:30, SEQ JD NO:47, SEQ JD NO:49, SEQ ID NO:51 and or SEQ ID NO:53;
• the antigenic determinant, fragment or functional equivalent of the sixth embodiment of the third aspect of the invention comprises one or more of the ten cysteine residues at amino acid positions 69, 82, 90, 92, 100, 105, 110, 120, 121 and 124 of SEQ ID NO:26. More preferably, one or more of these cysteine residues participate in disulphide bond formation under physiological conditions. Disulphide bond formation is often integral to the correct conformation of a protein and thus, its function. It is therefore important that such cysteine residues be conserved.
• the polypeptide having the sequence recited in SEQ ID NO: 18 is referred to hereafter as "the INSP125 exon 1 polypeptide".
• the polypeptide having the sequence recited in SEQ ID NO:20 is referred to hereafter as "the INSP125 exon 2 polypeptide”.
• the polypeptide having the sequence recited in SEQ JD NO:22 is referred to hereafter as "the INSP125 exon 3 polypeptide”.
• the polypeptide having the sequence recited in SEQ ID NO:24 is referred to hereafter as "the INSP125 exon 4 polypeptide".
• polypeptide having the sequence recited in SEQ JD NO:26 is referred to hereafter as "the FNSP125 polypeptide”.
• the Applicant does not wish to be bound by this theory, it is postulated that the first 22 amino acids of INSP125 cloned polypeptide form the signal peptide.
• the EMSP125 cloned full length polypeptide sequences with and without the signal sequence are recited in SEQ ID NO:55 and SEQ ED NO:57, respectively.
• the polypeptide having the sequence recited in SEQ ID NO:55 is referred to hereafter as "the INSP125 cloned polypeptide”.
• the polypeptide having the sequence recited in SEQ ID NO:57 is referred to hereafter as "the INSP125 cloned mature polypeptide 1".
• the Applicant does not wish to be bound by this theory, it is postulated that the first 21 amino acids of INSP125 cloned polypeptide form the signal peptide.
• the INSP125 cloned full length polypeptide sequences with and without the signal sequence are recited in SEQ ID NO:55 and SEQ JD NO:59, respectively.
• the polypeptide having the sequence recited in SEQ ID NO:55 is referred to hereafter as "the INSP125 cloned polypeptide”.
• the polypeptide having the sequence recited in SEQ ID NO:59 is referred to hereafter as "the INSP125 cloned mature polypeptide 2".
• the Applicant does not wish to be bound by this theory, it is postulated that the first 31 amino acids of INSP125 cloned polypeptide form the signal peptide.
• the INSP125 cloned full length polypeptide sequences with and without the signal sequence are recited in SEQ ID NO:55 and SEQ JD NO:61, respectively.
• the polypeptide having the sequence recited in SEQ ID NO:55 is referred to hereafter as "the INSP125 cloned polypeptide”.
• the polypeptide having the sequence recited in SEQ JD NO:61 is referred to hereafter as "the INSP125 cloned mature polypeptide 3".
• INSP125 exon polypeptides as used herein includes polypeptides comprising the INSP125 exon 1 polypeptide, INSP125 exon 1 mature polypeptide, the INSP125 exon 2 polypeptide, the, the INSP125 exon 3 polypeptide, the INSP125 exon 4 polypeptide, the INSP125 polypeptide, JNSP125 mature polypeptide 1, INSP125 mature polypeptide 2, or the INSP125 mature polypeptide 3, as well as polypeptides consisting of the INSP125 exon 1 polypeptide, the INSP125 exon 1 mature polypeptide, the INSP125 exon 2 polypeptide, the INSP125 exon 3 polypeptide, the INSP125 exon 4 polypeptide, the INSP125 polypeptide or the JJMSP125 mature polypeptide.
• the identification of novel proteins comprising vWFC domains is useful since such domains have been found to play an important role in a broad-cross section of diseases including those diseases associated with developmental processes such as those relating to cartilage and bone skeletal development.
• the invention provides a purified nucleic acid molecule which encodes a polypeptide of the second or third aspect of the invention.
• the purified nucleic acid molecule comprises the nucleic acid sequence as recited in SEQ JD NO:l (encoding the INSP123 polypeptide), SEQ JD NO:3 (encoding the INSP123 mature polypeptide), SEQ ID NO:5 (encoding the JJSTSP124 exon 1 polypeptide), SEQ ID NO:7 (encoding the INSP124 exon 2 polypeptide), SEQ ID NO:9 (encoding the INSP124 exon 3 polypeptide), SEQ ID NO:l l (encoding the INSP124 polypeptide), SEQ JD NO:13 (encoding the JNSP124 mature polypeptide), SEQ ID NO: 15 (encoding the FNSP124 exon 1 mature polypeptide), SEQ ID NO: 17 (encoding the INSP125 exon 1 polypeptide), SEQ ID NO:19 (encoding the INSP125 exon 2 polypeptide), SEQ JD NO:21 (encoding the INSP125 exon 3 polypeptide), SEQ ID NO:23 (encoding
• the invention further provides that the purified nucleic acid molecule consists of the nucleic acid sequence as recited in SEQ JD NO:l (encoding the INSP123 polypeptide), SEQ JD NO:3 (encoding the INSP123 mature polypeptide), SEQ ID NO:5 (encoding the INSP124 exon 1 polypeptide), SEQ ID NO:7 (encoding the INSP124 exon 2 polypeptide), SEQ JD NO:9 (encoding the INSP124 exon 3 polypeptide), SEQ JD NO:l l (encoding the INSP124 polypeptide), SEQ TD NO:13 (encoding the INSP124 mature polypeptide), SEQ TD NO:15 (encoding the INSP124 exon 1 mature polypeptide), SEQ ID NO: 17 (encoding the INSP125 exon 1 polypeptide), SEQ ID NO:19 (encoding the INSP125 exon 2 polypeptide), SEQ ID NO:21 (encoding the INSP125 exon 3 polypeptide), SEQ ID NO:23 (
• the purified nucleic acid molecule excludes the signal peptide located at the start of the EMSP123 polypeptide (amino acids 1 to 23 of SEQ ID NO:2), the INSP124 exon 1 polypeptide (amino acids 1 to 23 of SEQ ID NO:6), the INSP124 polypeptide (amino acids 1 to 23 of SEQ ID NO: 12), the INSP125 exon 1 polypeptide (amino acids 1 to 23 of SEQ ID NO:18) or the JNSP125 polypeptide (amino acids 1 to 23 of SEQ ID NO:26).
• the purified nucleic acid molecule preferably comprises nucleotides 70 to 417 of SEQ ID NO:l (shown in SEQ TD NO:3, encoding the INSP123 mature polypeptide), nucleotides 70 to 390 of SEQ ID NO:5 (shown in SEQ DD NO.T3, encoding the INSP124 exon 1 mature polypeptide), nucleotides 70 to 669 of SEQ DD NO:l l (shown in SEQ ID NO: 15, encoding the INSP124 mature polypeptide), nucleotides 70 to 100 of SEQ ID NO: 17, (shown in SEQ ID NO:27, encoding the INSP125 exon 1 mature polypeptide) or nucleotides 70 to 528 of SEQ ID NO:25 (shown in SEQ ID NO:29, encoding the INSP125 mature polypeptide).
• the purified nucleic acid molecule excludes the signal peptide located at the start of the INSP123 polypeptide (amino acids 1 to 22 of SEQ JD NO:39), the JNSP124 polypeptide (amino acids 1 to 22 of SEQ JD NO:43), or the INSP125 polypeptide (amino acids 1 to 22 of SEQ ID NO:47).
• the purified nucleic acid molecule preferably comprises nucleotides 67 to 414 of SEQ ID NO:38 (shown in SEQ ID NO:40, encoding the INSP123 cloned mature polypeptide 1), nucleotides 67 to 666 of SEQ TD NO:46 (shown in SEQ ID NO:48, encoding the INSP124 cloned mature polypeptide 1), or nucleotides 67 to 525 of SEQ ID NO:54 (shown in SEQ ID NO:56, encoding the INSP125 cloned mature polypeptide 1).
• the purified nucleic acid molecule excludes the signal peptide located at the start of the INSP123 polypeptide (amino acids 1 to 21 of SEQ ID NO:39), the TNSP124 polypeptide (amino acids 1 to 21 of SEQ ID NO:47), or the INSP125 polypeptide (amino acids 1 to 21 of SEQ ID NO:55).
• the purified nucleic acid molecule preferably comprises nucleotides 64 to 414 of SEQ ED NO:38 (shown in SEQ ID NO:42, encoding the INSP123 cloned mature polypeptide 2), nucleotides 44 to 666 of SEQ ID NO:46 (shown in SEQ ID NO:50, encoding the INSP124 cloned mature polypeptide 2), or nucleotides 64 to 525 of SEQ ID NO:54 (shown in SEQ ID NO:58, encoding the INSP125 cloned mature polypeptide 2).
• the purified nucleic acid molecule excludes the signal peptide located at the start of the INSP123 polypeptide (amino acids 1 to 31 of SEQ ID NO:39), the INSP124 polypeptide (amino acids 1 to
• the purified nucleic acid molecule preferably comprises nucleotides
• the invention further provides a purified nucleic acid molecule consisting of nucleotides 70 to 417 of SEQ ID NO:l (shown in SEQ ED NO:3, encoding the INSP123 mature polypeptide), nucleotides 70 to 390 of SEQ ED NO:5 (shown in SEQ ID NO:13, encoding the INSP124 exon 1 mature polypeptide), nucleotides 70 to 669 of SEQ ID NO: 11 (shown in SEQ ID NO: 15, encoding the INSP124 mature polypeptide), nucleotides 70 to 100 of SEQ ID NO:17, (shown in SEQ ED NO:27, encoding the INSP125 exon 1 mature polypeptide), nucleotides 70 to 528 of SEQ ID NO:25 (shown in SEQ JD NO:29, encoding the INSP125 mature polypeptide), nucleotides 67 to 414 of SEQ ID NO:38 (shown in SEQ ED NO:40, encoding the IN
• the invention provides a purified nucleic acid molecule which hybridizes under high stringency conditions with a nucleic acid molecule of the fourth aspect of the invention.
• the invention provides a vector, such as an expression vector, that contains a nucleic acid molecule of the fourth or fifth aspect of the invention.
• Preferred vectors include pCR4-TOPO-INSP123 (figure 9), pDONR (figure 10), pEAK12d (figure 11), pDEST12.2 (figure 12), pENTR-INSP123-6HIS (figure 13), pEAK12d-INSP123-6HIS (figure 14), pDEST12.2- INSP123-6HIS (figure 15), pCR4-BluntII-TOPO-INSP124 (figure 19), pDONR 221 (figure 20), pEAK12d (figure 21), pDEST12.2 (figure 22), pENTR NSP124-6HIS (figure 23), pEAK12d_INSP124-6HIS (figure 24), pDEST12.2_ INSP124-6HIS (figure 25), pCR4-TOPO-INS
• the invention provides a host cell transformed with a vector of the sixth aspect of the invention.
• the invention provides a ligand which binds specifically to a member of the vWFC domain containing protein family of the second or third aspect of the invention.
• the invention provides a compound that is effective to alter the expression of a natural gene which encodes a polypeptide of the second or third aspect of the invention or to regulate the activity of a polypeptide of the second or third aspect of the invention.
• a compound of the ninth aspect of the invention may either increase (agonise) or decrease (antagonise) the level of expression of the gene or the activity of the polypeptide.
• the identification of the function of the 1NSP123, TNSP124 and EMSP125 polypeptides allows for the design of screening methods capable of identifying compounds that are effective in the treatment and/or diagnosis of disease.
• Ligands and compounds according to the eighth and ninth aspects of the invention may be identified using such methods. These methods are included as aspects of the present invention.
• the invention provides a polypeptide of the second or third aspect of the invention, or a nucleic acid molecule of the fourth or fifth aspect of the invention, or a vector of the sixth aspect of the invention, or a host cell of the seventh aspect of the invention, or a ligand of the eighth aspect of the invention, or a compound of the ninth aspect of the invention, for use in therapy or diagnosis of diseases in which members of the vWFC domain containing protein family are implicated.
• Such diseases may include cell proliferative disorders, including neoplasm, melanoma, lung, colorectal, breast, pancreas, head and neck and other solid tumours; myeloproliferative disorders, such as leukemia, non-Hodgkin lymphoma, leukopenia, thrombocytopenia, angiogenesis disorder, Kaposis' sarcoma; autoimmune/inflarnmatory disorders, including allergy, inflammatory bowel disease, arthritis, psoriasis and respiratory tract inflammation, asthma, and organ transplant rejection; cardiovascular disorders, including hypertension, oedema, angina, atherosclerosis, thrombosis, sepsis, shock, reperfusion injury, and ischemia; neurological disorders including central nervous system disease, Alzheimer's disease, brain injury, amyotrophic lateral sclerosis, and pain; developmental disorders such as those relating to cartilage and bone skeletal development, including osteoarthritis; metabolic disorders including diabetes mellitus, osteoporosis,
• the diseases are those in which vWFC domain containing proteins are implicated.
• These molecules may also be used in the manufacture of a medicament for the treatment of such diseases.
• These molecules may also be used in contraception or for the treatment of reproductive disorders including infertility.
• the invention provides a method of diagnosing a disease in a patient, comprising assessing the level of expression of a natural gene encoding a polypeptide of the second or third aspect of the invention or the activity of a polypeptide of the second or third aspect of the invention in tissue from said patient and comparing said level of expression or activity to a control level, wherein a level that is different to said control level is indicative of disease.
• a method will preferably be carried out in vitro.
• Similar methods may be used for monitoring the therapeutic treatment of disease in a patient, wherein altering the level of expression or activity of a polypeptide or nucleic acid molecule over the period of time towards a control level is indicative of regression of disease.
• a preferred method for detecting polypeptides of the second or third aspect of the invention comprises the steps of: (a) contacting a ligand, such as an antibody, of the eighth aspect of the invention with a biological sample under conditions suitable for the formation of a ligand- polypeptide complex; and (b) detecting said complex.
• a number of different such methods according to the eleventh aspect of the invention exist, as the skilled reader will be aware, such as methods of nucleic acid hybridization with short probes, point mutation analysis, polymerase chain reaction (PCR) amplification and methods using antibodies to detect aberrant protein levels. Similar methods may be used on a short or long term basis to allow therapeutic treatment of a disease to be monitored in a patient.
• the invention also provides kits that are useful in these methods for diagnosing disease.
• the invention provides for the use of a polypeptide of the second or third aspect of the invention as a vWFC domain containing protein.
• Suitable uses of the polypeptides of the invention as vWFC domain containing proteins include use as a regulator of cellular growth, metabolism or differentiation, use as part of a receptor/ligand pair and use as a diagnostic marker for a physiological or pathological condition.
• the invention provides a pharmaceutical composition
• a pharmaceutical composition comprising a polypeptide of the second or third aspect of the invention, or a nucleic acid molecule of the fourth or fifth aspect of the invention, or a vector of the sixth aspect of the invention, or a host cell of the seventh aspect of the invention, or a ligand of the eighth aspect of the invention, or a compound of the ninth aspect of the invention, in conjunction with a pharmaceutically-acceptable carrier.
• the present invention provides a polypeptide of the second or third aspect of the invention, or a nucleic acid molecule of the fourth or fifth aspect of the invention, or a vector of the sixth aspect of the invention, or a host cell of the seventh aspect of the invention, or a ligand of the eighth aspect of the invention, or a compound of the ninth aspect of the invention, for use in the manufacture of a medicament for the diagnosis or treatment of a disease.
• the invention provides a method of treating a disease in a patient comprising administering to the patient a polypeptide of the second or third aspect of the invention, or a nucleic acid molecule of the fourth or fifth aspect of the invention, or a vector of the sixth aspect of the invention, or a host cell of the seventh aspect of the invention, or a ligand of the eighth aspect of the invention, or a compound of the ninth aspect of the invention.
• the polypeptide, nucleic acid molecule, ligand or compound administered to the patient should be an agonist.
• the polypeptide, nucleic acid molecule, ligand or compound administered to the patient should be an antagonist.
• antagonists include antisense nucleic acid molecules, ribozymes and ligands, such as antibodies.
• the invention provides transgenic or knockout non-human animals that have been transformed to express higher, lower or absent levels of a polypeptide of the second or third aspect of the invention.
• Such transgenic animals are very useful models for the study of disease and may also be used in screening regimes for the identification of compounds that are effective in the treatment or diagnosis of such a disease.
• polypeptide includes any peptide or protein comprising two or more amino acids joined to each other by peptide bonds or modified peptide bonds, i.e. peptide isosteres. This term refers both to short chains (peptides and oligopeptides) and to longer chains (proteins).
• the polypeptide of the present invention may be in the form of a mature protein or may be a pre-, pro- or prepro- protein that can be activated by cleavage of the pre-, pro- or prepro- portion to produce an active mature polypeptide.
• the pre-, pro- or prepro- sequence may be a leader or secretory sequence or may be a sequence that is employed for purification of the mature polypeptide sequence.
• polypeptide of the second or third aspect of the invention may form part of a fusion protein.
• additional amino acid sequences which may contain secretory or leader sequences, pro-sequences, sequences which aid in purification, or sequences that confer higher protein stability, for example during recombinant production.
• the mature polypeptide may be fused with another compound, such as a compound to increase the half-life of the polypeptide (for example, polyethylene glycol).
• Polypeptides may contain amino acids other than the 20 gene-encoded amino acids, modified either by natural processes, such as by post-translational processing or by chemical modification techniques which are well known in the art.
• modifications which may commonly be present in polypeptides of the present invention are glycosylation, lipid attachment, sulphation, garnma-carboxylation, for instance of glutamic acid residues, hydroxylation and ADP- ribosylation.
• Modifications can occur anywhere in a polypeptide, including the peptide backbone, the amino acid side-chains and the amino or carboxyl termini.
• blockage of the amino or carboxyl terminus in a polypeptide, or both, by a covalent modification is common in naturally-occurring and synthetic polypeptides and such modifications may be present in polypeptides of the present invention.
• modifications that occur in a polypeptide often will be a function of how the polypeptide is made.
• the nature and extent of the modifications in large part will be determined by the post-translational modification capacity of the particular host cell and the modification signals that are present in the amino acid sequence of the polypeptide in question. For instance, glycosylation patterns vary between different types of host cell.
• polypeptides of the present invention can be prepared in any suitable manner.
• Such polypeptides include isolated naturally-occurring polypeptides (for example purified from cell culture), recombinantly-produced polypeptides (including fusion proteins), synthetically-produced polypeptides or polypeptides that are produced by a combination of these methods.
• the functionally-equivalent polypeptides of the third aspect of the invention may be polypeptides that are homologous to the INSP123, INSP124 and INSP125 polypeptides.
• Two polypeptides are said to be "homologous", as the term is used herein, if the sequence of one of the polypeptides has a high enough degree of identity or similarity to the sequence of the other polypeptide. "Identity” indicates that at any particular position in the aligned sequences, the amino acid residue is identical between the sequences. "Similarity” indicates that, at any particular position in the aligned sequences, the amino acid residue is of a similar type between the sequences. Degrees of identity and similarity can be readily calculated (Computational Molecular Biology, Lesk, A.M., ed.,
• Homologous polypeptides therefore include natural biological variants (for example, allelic variants or geographical variations within the species from which the polypeptides are derived) and mutants (such as mutants containing amino acid substitutions, insertions or deletions) of the INSP123, INSP124 and INSP125 polypeptides.
• Such mutants may include polypeptides in which one or more of the amino acid residues are substituted with a conserved or non-conserved amino acid residue (preferably a conserved amino acid residue) and such substituted amino acid residue may or may not be one encoded by the genetic code.
• Such substitutions are among Ala, Val, Leu and Ile; among Ser and Thr; among the acidic residues Asp and Glu; among Asn and Gin; among the basic residues Lys and Arg; or among the aromatic residues Phe and Tyr.
• Particularly preferred are variants in which several, i.e. between 5 and 10, 1 and 5, 1 and 3, 1 and 2 or just 1 amino acids are substituted, deleted or added in any combination.
• silent substitutions, additions and deletions which do not alter the properties and activities of the protein. Also especially preferred in this regard are conservative substitutions.
• Such mutants also include polypeptides in which one or more of the amino acid residues includes a substituent group.
• polypeptides of the second or third aspect of the invention have a degree of sequence identity with the JNSP123, JNSP124 or TNSP125 polypeptides, or with active fragments thereof, of greater than 80%. More preferred polypeptides have degrees of identity of greater than 85%, 90%, 95%, 98% or 99%, respectively.
• the functionally-equivalent polypeptides of the second or third aspect of the invention may also be polypeptides which have been identified using one or more techniques of structural alignment.
• the Inpharmatica Genome Threader technology that forms one aspect of the search tools used to generate the BiopendiumTM search database may be used (see PCT application WO 01/69507) to identify polypeptides of presently-unknown function which, while having low sequence identity as compared to the INSP123, ESTSP124 and JNSP125 polypeptides, are predicted to be members of the vWFC domain containing protein family, by virtue of sharing significant structural homology with the INSP123, INSP124 and INSP125 polypeptide sequences.
• significant structural homology is meant that the Inpharmatica Genome Threader predicts two proteins to share structural homology with a certainty of 10% and above.
• polypeptides of the second or third aspect of the invention also include fragments of the INSP123, JNSP124 and INSP125 polypeptides and fragments of the functional equivalents of the JNSP123, INSP124 and TNSP125 polypeptides, provided that those fragments are members of the vWFC containing protein family or have an antigenic determinant in common with the INSP123, INSP124 and E SP125 polypeptides.
• fragment refers to a polypeptide having an amino acid sequence that is the same as part, but not all, of the amino acid sequence of the INSP123, INSP124, and INSP125 polypeptides or one of their functional equivalents.
• the fragments should comprise at least n consecutive amino acids from the sequence and, depending on the particular sequence, n preferably is 7 or more (for example, 8, 10, 12, 14, 16, 18, 20 or more). Small fragments may form an antigenic determinant.
• Fragments of the full length INSP123, INSP124 and INSP125 polypeptides may consist of combinations of 2, 3 or 4 of neighbouring exon sequences in the INSP123, INSP124, and INSP125 polypeptide sequences, respectively.
• fragments may be "free-standing", i.e. not part of or fused to other amino acids or polypeptides, or they may be comprised within a larger polypeptide of which they form a part or region.
• the fragment of the invention When comprised within a larger polypeptide, the fragment of the invention most preferably forms a single continuous region.
• certain preferred embodiments relate to a fragment having a pre- and/or pro- polypeptide region fused to the amino terminus of the fragment and or an additional region fused to the carboxyl terminus of the fragment.
• several fragments may be comprised within a single larger polypeptide.
• polypeptides of the present invention or their immunogenic fragments can be used to generate ligands, such as polyclonal or monoclonal antibodies, that are immunospecific for the polypeptides.
• ligands such as polyclonal or monoclonal antibodies
• Such antibodies may be employed to isolate or to identify clones expressing the polypeptides of the invention or to purify the polypeptides by affinity chromatography.
• the antibodies may also be employed as diagnostic or therapeutic aids, amongst other applications, as will be apparent to the skilled reader.
• protein means a type of polypeptide including, but not limited to those that function as enzymes.
• the protein or polypeptide of the present invention functions as a ligand.
• a ligand in this context means a molecule that binds to another molecule, such as a receptor.
• a ligand may be a co-factor for an enzyme.
• immunospecific means that the antibodies have substantially greater affinity for the polypeptides of the invention than their affinity for other related polypeptides in the prior art.
• antibody refers to intact molecules as well as to fragments thereof, such as Fab, F(ab')2 and Fv, which are capable of binding to the antigenic determinant in question. Such antibodies thus bind to the polypeptides of the second or third aspect of the invention.
• a selected mammal such as a mouse, rabbit, goat or horse
• a polypeptide of the second or third aspect of the invention may be immunised with a polypeptide of the second or third aspect of the invention.
• the polypeptide used to immunise the animal can be derived by recombinant DNA technology or can be synthesized chemically.
• the polypeptide can be conjugated to a carrier protein.
• Commonly used carriers to which the polypeptides may be chemically coupled include bovine serum albumin, thyroglobulin and keyhole limpet haemocyanin.
• the coupled polypeptide is then used to immunise the animal. Serum from the immunised animal is collected and treated according to known procedures, for example by immunoaffinity chromatography.
• Monoclonal antibodies to the polypeptides of the second or third aspect of the invention can also be readily produced by one skilled in the art.
• the general methodology for making monoclonal antibodies using hybridoma technology is well known (see, for example, Kohler, G. and Milstein, C, Nature 256: 495-497 (1975); Kozbor et al, Immunology Today 4: 72 (1983); Cole et al, 77-96 in Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, Inc. (1985).
• Panels of monoclonal antibodies produced against the polypeptides of the second or third aspect of the invention can be screened for various properties, i.e., for isotype, epitope, affinity, etc. Monoclonal antibodies are particularly useful in purification of the individual polypeptides against which they are directed. Alternatively, genes encoding the monoclonal antibodies of interest may be isolated from hybridomas, for instance by PCR techniques known in the art, and cloned and expressed in appropriate vectors.
• Chimeric antibodies in which non-human variable regions are joined or fused to human constant regions (see, for example, Liu et al, Proc. Natl. Acad. Sci. USA, 84, 3439 (1987)), may also be of use.
• the antibody may be modified to make it less immunogenic in an individual, for example by humanisation (see Jones et al, Nature, 321, 522 (1986); Verhoeyen et al, Science, 239, 1534 (1988); Kabat et al, J. Immunol., 147, 1709 (1991); Queen et al, Proc. Natl Acad. Sci. USA, 86, 10029 (1989); Gorman et al, Proc. Natl Acad. Sci. USA, 88, 34181 (1991); and Hodgson et al, Bio/Technology, 9, 421 (1991)).
• humanisation see Jones et al, Nature, 321, 522 (1986); Verhoeyen et al, Science, 239, 1534 (1988); Kabat et al, J. Immunol., 147, 1709 (1991); Queen et al, Proc. Natl Acad. Sci. USA, 86, 10029 (1989); Gorman et
• humanised antibody refers to antibody molecules in which the CDR amino acids and selected other amino acids in the variable domains of the heavy and/or light chains of a non-human donor antibody have been substituted in place of the equivalent amino acids in a human antibody.
• the humanised antibody thus closely resembles a human antibody but has the binding ability of the donor antibody.
• the antibody may be a "bispecific" antibody, that is an antibody having two different antigen binding domains, each domain being directed against a different epitope.
• Phage display technology may be utilised to select genes which encode antibodies with binding activities towards the polypeptides of the invention either from repertoires of PCR amplified V- genes of lymphocytes from humans screened for possessing the relevant antibodies, or from naive libraries (McCafferty, J. et al, (1990), Nature 348, 552-554; Marks, J. et al, (1992) Biotechnology 10, 779-783).
• the affinity of these antibodies can also be improved by chain shuffling (Clackson, T. et al, (1991) Nature 352, 624-628).
• Antibodies generated by the above techniques have additional utility in that they may be employed as reagents in immunoassays, radioimmunoassays (RIA) or enzyme-linked immunosorbent assays (ELISA).
• the antibodies can be labelled with an analytically-detectable reagent such as a radioisotope, a fluorescent molecule or an enzyme.
• Preferred nucleic acid molecules of the fourth and fifth aspects of the invention are those which encode a polypeptide sequence as recited in SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO: 10, SEQ ID NO:12, SEQ ED NO:14, SEQ ID NO:16, SEQ ID NO:18, SEQ ID NO:20, SEQ ID NO:22, SEQ ED NO:24, SEQ ID NO:26, SEQ ID NO:28, SEQ JD NO:30, SEQ JD NO:28, SEQ TD NO:30, SEQ JD NO:39, SEQ JD NO:41, SEQ JD NO:43, SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ JD NO:53, SEQ JD NO:55, SEQ ID NO:57, SEQ ID NO:59 and SEQ ED NO:61 and functionally equivalent polypeptides.
• nucleic acid molecules may be used in the methods and applications described herein.
• the nucleic acid molecules of the invention preferably comprise at least n consecutive nucleotides from the sequences disclosed herein where, depending on the particular sequence, n is 10 or more (for example, 12, 14, 15, 18, 20, 25, 30, 35, 40 or more).
• nucleic acid molecules of the invention also include sequences that are complementary to nucleic acid molecules described above (for example, for antisense or probing pu ⁇ oses).
• Nucleic acid molecules of the present invention may be in the form of RNA, such as mRNA, or in the form of DNA, including, for instance cDNA, synthetic DNA or genomic DNA. Such nucleic acid molecules may be obtained by cloning, by chemical synthetic techniques or by a combination thereof. The nucleic acid molecules can be prepared, for example, by chemical synthesis using techniques such as solid phase phosphoramidite chemical synthesis, from genomic or cDNA libraries or by separation from an organism. RNA molecules may generally be generated by the in vitro or in vivo transcription of DNA sequences.
• the nucleic acid molecules may be double-stranded or single-stranded.
• Single-stranded DNA may be the coding strand, also known as the sense strand, or it may be the non-coding strand, also referred to as the anti-sense strand.
• nucleic acid molecule also includes analogues of DNA and RNA, such as those containing modified backbones, and peptide nucleic acids (PNA).
• PNA peptide nucleic acids
• PNAs may be pegylated to extend their lifespan in a cell, where they preferentially bind complementary single stranded DNA and RNA and stop transcript elongation (Nielsen, P.E. et al. (1993) Anticancer Drug Des. 8:53-63).
• a nucleic acid molecule which encodes a polypeptide of this invention may be identical to the coding sequence of one or more of the nucleic acid
• These molecules also may have a different sequence which, as a result of the degeneracy of the genetic code, encodes a polypeptide SEQ ED NO:2, SEQ TD NO:4, SEQ ED NO:6, SEQ ID NO:8, SEQ ED NO:10, SEQ ED NO:12, SEQ ID NO:14, SEQ JD N0.16, SEQ JD NO:18, SEQ JD NO:20, SEQ JD NO:22, SEQ JD NO:24, SEQ ED NO:26, SEQ JD NO:28, SEQ ED NO:30 SEQ ID NO:39, SEQ ED NO:41, SEQ ED NO:43, SEQ ED NO:45, SEQ ID NO:47, SEQ ED NO:49, SEQ ID NO:51, SEQ ID NO:53, SEQ ID NO:55, SEQ JD NO:57, SEQ ED NO:59 and/or SEQ ID NO:61.
• nucleic acid molecules may include, but are not limited to, the coding sequence for the mature polypeptide by itself; the coding sequence for the mature polypeptide and additional coding sequences, such as those encoding a leader or secretory sequence, such as a pro-, pre- or prepro- polypeptide sequence; the coding sequence of the mature polypeptide, with or without the aforementioned additional coding sequences, together with further additional, non-coding sequences, including non-coding 5' and 3' sequences, such as the transcribed, non-translated sequences that play a role in transcription (including termination signals), ribosome binding and mRNA stability.
• the nucleic acid molecules may also include additional sequences which encode additional amino acids, such as those which provide additional functionalities.
• nucleic acid molecules of the fourth and fifth aspects of the invention may also encode the fragments or the functional equivalents of the polypeptides and fragments of the second or third aspect of the invention.
• a nucleic acid molecule may be a naturally-occurring variant such as a naturally-occurring allelic variant, or the molecule may be a variant that is not known to occur naturally.
• non-naturally occurring variants of the nucleic acid molecule may be made by mutagenesis techniques, including those applied to nucleic acid molecules, cells or organisms.
• variants in this regard are variants that differ from the aforementioned nucleic acid molecules by nucleotide substitutions, deletions or insertions.
• the substitutions, deletions or insertions may involve one or more nucleotides.
• the variants may be altered in coding or non- coding regions or both. Alterations in the coding regions may produce conservative or non- conservative amino acid substitutions, deletions or insertions.
• the nucleic acid molecules of the invention can also be engineered, using methods generally known in the art, for a variety of reasons, including modifying the cloning, processing, and/or expression of the gene product (the polypeptide).
• DNA shuffling by random fragmentation and PCR reassembly of gene fragments and synthetic oligonucleotides are included as techniques which may be used to engineer the nucleotide sequences.
• Site-directed mutagenesis may be used to insert new restriction sites, alter glycosylation patterns, change codon preference, produce splice variants, introduce mutations and so forth.
• Nucleic acid molecules which encode a polypeptide of the second or third aspect of the invention may be ligated to a heterologous sequence so that the combined nucleic acid molecule encodes a fusion protein.
• Such combined nucleic acid molecules are included within the fourth or fifth aspects of the invention.
• a fusion protein that can be recognised by a commercially-available antibody.
• a fusion protein may also be engineered to contain a cleavage site located between the sequence of the polypeptide of the invention and the sequence of a heterologous protein so that the polypeptide may be cleaved and purified away from the heterologous protein.
• the nucleic acid molecules of the invention also include antisense molecules that are partially complementary to nucleic acid molecules encoding polypeptides of the present invention and that therefore hybridize to the encoding nucleic acid molecules (hybridization).
• antisense molecules such as oligonucleotides, can be designed to recognise, specifically bind to and prevent transcription of a target nucleic acid encoding a polypeptide of the invention, as will be known by those of ordinary skill in the art (see, for example, Cohen, J.S., Trends in Pharm. Sci., 10, 435 (1989), Okano, J. Neurochem. 56, 560 (1991); O'Connor, J. Neurochem 56, 560 (1991); Lee et al, Nucleic Acids Res 6, 3073 (1979); Cooney et al, Science 241, 456 (1988); Dervan et al, Science 251, 1360 (1991).
• hybridization refers to the association of two nucleic acid molecules with one another by hydrogen bonding. Typically, one molecule will be fixed to a solid support and the other will be free in solution. Then, the two molecules may be placed in contact with one another under conditions that favour hydrogen bonding. Factors that affect this bonding include: the type and volume of solvent; reaction temperature; time of hybridization; agitation; agents to block the non-specific attachment of the liquid phase molecule to the solid support (Denhardt's reagent or BLOTTO); the concentration of the molecules; use of compounds to increase the rate of association of molecules (dextran sulphate or polyethylene glycol); and the stringency of the washing conditions following hybridization (see Sambrook et al. [supra]).
• the inhibition of hybridization of a completely complementary molecule to a target molecule may be examined using a hybridization assay, as known in the art (see, for example, Sambrook et al [supra]).
• a substantially homologous molecule will then compete for and inhibit the binding of a completely homologous molecule to the target molecule under various conditions of stringency, as taught in Wahl, G.M. and S.L. Berger (1987; Methods Enzymol. 152:399-407) and Ki mel, A.R. (1987; Methods Enzymol. 152:507-511).
• Stringency refers to conditions in a hybridization reaction that favour the association of very similar molecules over association of molecules that differ.
• High stringency hybridisation conditions are defined as overnight incubation at 42°C in a solution comprising 50% formamide, 5XSSC (150mM NaCl, 15mM trisodium citrate), 50mM sodium phosphate (pH7.6), 5x Denhardts solution, 10% dextran sulphate, and 20 microgram/ml denatured, sheared salmon sperm DNA, followed by washing the filters in 0.1X SSC at approximately 65°C.
• Low stringency conditions involve the hybridisation reaction being carried out at 35°C (see Sambrook et al. [supra]).
• the conditions used for hybridization are those of high stringency.
• nucleic acid molecules that are at least 70% identical over their entire length to a nucleic acid molecule encoding the L SP123, INSP124 or INSP125 polypeptides and nucleic acid molecules that are substantially complementary to such nucleic acid molecules.
• a nucleic acid molecule according to this aspect of the invention comprises a region that is at least 80% identical over its entire length to such coding sequences, or is a nucleic acid molecule that is complementary thereto.
• nucleic acid molecules at least 90%, preferably at least 95%, more preferably at least 98%, 99% or more identical over their entire length to the same are particularly preferred.
• Preferred embodiments in this respect are nucleic acid molecules that encode polypeptides which retain substantially the same biological function or activity as the INSP123, INSP124 and INSP125 polypeptides.
• the invention also provides a process for detecting a nucleic acid molecule of the invention, comprising the steps of: (a) contacting a nucleic probe according to the invention with a biological sample under hybridizing conditions to form duplexes; and (b) detecting any such duplexes that are formed.
• a nucleic acid molecule as described above may be used as a hybridization probe for RNA, cDNA or genomic DNA, in order to isolate full-length cDNAs and genomic clones encoding the TNSP123, INSP124 and INSP125 polypeptides and to isolate cDNA and genomic clones of homologous or orthologous genes that have a high sequence similarity to the gene encoding this polypeptide.
• the sequencing process may be automated using machines such as the Hamilton Micro Lab 2200 (Hamilton, Reno, NV), the Peltier Thermal Cycler (PTC200; MJ Research, Watertown, MA) and the ABI Catalyst and 373 and 377 DNA Sequencers (Perkin Elmer).
• machines such as the Hamilton Micro Lab 2200 (Hamilton, Reno, NV), the Peltier Thermal Cycler (PTC200; MJ Research, Watertown, MA) and the ABI Catalyst and 373 and 377 DNA Sequencers (Perkin Elmer).
• One method for isolating a nucleic acid molecule encoding a polypeptide with an equivalent function to that of the JNSP123, JNSP124 and ENSP125 polypeptides is to probe a genomic or cDNA library with a natural or artificially-designed probe using standard procedures that are recognised in the art (see, for example, "Current Protocols in Molecular Biology", Ausubel et al. (eds). Greene Publishing Association and John Wiley Interscience, New York, 1989,1992).
• Probes comprising at least 15, preferably at least 30, and more preferably at least 50, contiguous bases that correspond to, or are complementary to, nucleic acid sequences from the appropriate encoding gene (SEQ EDNO:l, SEQ D O:3, SEQ IDNO:5, SEQ ED NO:7, SEQ ID NO:9, SEQ ED NO:l l, SEQ D NO:13, SEQ JD NO:15, SEQ JD NO:17, SEQ ID NO:19, SEQ ED NO:21, SEQ ED NO:23, SEQ ID NO:25, SEQ ED NO:27, SEQ ID NO:29, SEQ ED NO:38, SEQ ED NO:40, SEQ ID NO:42, SEQ ED NO:44, SEQ ID NO:46, SEQ ED NO:48, SEQ ID NO:50, SEQ JD NO:52, SEQ JD NO:54, SEQ JD NO:56, SEQ JD NO:58 and SEQ ED NO:60), are
• Such probes may be labelled with an analytically-detectable reagent to facilitate their identification.
• Useful reagents include, but are not limited to, radioisotopes, fluorescent dyes and enzymes that are capable of catalysing the formation of a detectable product.
• the ordinarily skilled artisan will be capable of isolating complementary copies of genomic DNA, cDNA or RNA polynucleotides encoding proteins of interest from human, mammalian or other animal sources and screening such sources for related sequences, for example, for additional members of the family, type and/or subtype.
• isolated cDNA sequences will be incomplete, in that the region encoding the polypeptide will be cut short, normally at the 5' end.
• Several methods are available to obtain full length cDNAs, or to extend short cDNAs. Such sequences may be extended utilising a partial nucleotide sequence and employing various methods known in the art to detect upstream sequences such as promoters and regulatory elements. For example, one method which may be employed is based on the method of Rapid Amplification of cDNA Ends (RACE; see, for example, Frohman et al, PNAS USA 85, 8998-9002, 1988).
• RACE Rapid Amplification of cDNA Ends
• Another method which may be used is capture PCR which involves PCR amplification of DNA fragments adjacent a known sequence in human and yeast artificial chromosome DNA (Lagerstrom, M. et al. (1991) PCR Methods Applic, 1, 111-119). Another method which may be used to retrieve unknown sequences is that of Parker, JD. et al. (1991); Nucleic Acids Res. 19:3055-3060). Additionally, one may use PCR, nested primers, and PromoterFinderTM libraries to walk genomic DNA (Clontech, Palo Alto, CA). This process avoids the need to screen libraries and is useful in finding intron/exon junctions.
• libraries that have been size-selected to include larger cDNAs.
• random-primed libraries are preferable, in that they will contain more sequences that contain the 5' regions of genes. Use of a randomly primed library may be especially preferable for situations in which an oligo d(T) library does not yield a full-length cDNA.
• Genomic libraries may be useful for extension of sequence into 5' non-transcribed regulatory regions.
• the nucleic acid molecules of the present invention may be used for chromosome localisation.
• a nucleic acid molecule is specifically targeted to, and can hybridize with, a particular location on an individual human chromosome.
• the mapping of relevant sequences to chromosomes according to the present invention is an important step in the confirmatory correlation of those sequences with the gene-associated disease. Once a sequence has been mapped to a precise chromosomal location, the physical position of the sequence on the chromosome can be correlated with genetic map data. Such data are found in, for example, V. McKusick, Mendelian Inheritance in Man (available on-line through Johns Hopkins University Welch Medical Library).
• the relationships between genes and diseases that have been mapped to the same chromosomal region are then identified through linkage analysis (coinheritance of physically adjacent genes). This provides valuable information to investigators searching for disease genes using positional cloning or other gene discovery techniques. Once the disease or syndrome has been crudely localised by genetic linkage to a particular genomic region, any sequences mapping to that area may represent associated or regulatory genes for further investigation.
• the nucleic acid molecule may also be used to detect differences in the chromosomal location due to translocation, inversion, etc. among normal, carrier, or affected individuals.
• the nucleic acid molecules of the present invention are also valuable for tissue localisation.
• Such techniques allow the determination of expression patterns of the polypeptide in tissues by detection of the mRNAs that encode them.
• These techniques include in situ hybridization techniques and nucleotide amplification techniques, such as PCR. Results from these studies provide an indication of the normal functions of the polypeptide in the organism.
• comparative studies of the normal expression pattern of mRNAs with that of mRNAs encoded by a mutant gene provide valuable insights into the role of mutant polypeptides in disease. Such inappropriate expression may be of a temporal, spatial or quantitative nature.
• the vectors of the present invention comprise nucleic acid molecules of the invention and may be cloning or expression vectors.
• the host cells of the invention which may be transformed, transfected or transduced with the vectors of the invention may be prokaryotic or eukaryotic.
• polypeptides of the invention may be prepared in recombinant form by expression of their encoding nucleic acid molecules in vectors contained within a host cell. Such expression methods are well known to those of skill in the art and many are described in detail by Sambrook et al (supra) and Fernandez & Hoeffler (1998, eds. "Gene expression systems. Using nature for the art of expression”. Academic Press, San Diego, London, Boston, New York, Sydney, Tokyo, Toronto).
• any system or vector that is suitable to maintain, propagate or express nucleic acid molecules to produce a polypeptide in the required host may be used.
• the appropriate nucleotide sequence may be inserted into an expression system by any of a variety of well-known and routine techniques, such as, for example, those described in Sambrook et al, (supra).
• the encoding gene can be placed under the control of a control element such as a promoter, ribosome binding site (for bacterial expression) and, optionally, an operator, so that the DNA sequence encoding the desired polypeptide is transcribed into RNA in the transformed host cell.
• suitable expression systems include, for example, chromosomal, episomal and virus- derived systems, including, for example, vectors derived from: bacterial plasmids, bacteriophage, transposons, yeast episomes, insertion elements, yeast chromosomal elements, viruses such as baculoviruses, papova viruses such as SV40, vaccinia viruses, adenoviruses, fowl pox viruses, pseudorabies viruses and retroviruses, or combinations thereof, such as those derived from plasmid and bacteriophage genetic elements, including cosmids and phagemids.
• HACs Human artificial chromosomes
• pEAK12d (figure 21), pDEST12.2 (figure 22), pENTR_INSP124-6HIS (figure 23), pEAK12d_INSP124-6HIS (figure 24), pDEST12.2_ INSP124-6HIS (figure 25), pCR4-TOPO-INSP125 (figure 29), pDONR 221 (figure 30), pEAK12d (figure 31), pDEST12.2 (figure 32), pENTR NSP125-6HIS (figure 33), pEAK12d_JNSP125- 6HIS (figure 34) and pDEST12.2_ INSP125-6HIS (figure 35) are preferred examples of suitable vectors for use in accordance with the invention.
• Particularly suitable expression systems include microorganisms such as bacteria transformed with recombinant bacteriophage, plasmid or cosmid DNA expression vectors; yeast transformed with yeast expression vectors; insect cell systems infected with virus expression vectors (for example, baculovirus); plant cell systems transformed with virus expression vectors (for example, cauliflower mosaic virus, CaMV; tobacco mosaic virus, TMV) or with bacterial expression vectors (for example, Ti or pBR322 plasmids); or animal cell systems.
• Cell-free translation systems can also be employed to produce the polypeptides of the invention.
• nucleic acid molecules encoding a polypeptide of the present invention into host cells can be effected by methods described in many standard laboratory manuals, such as Davis et al, Basic Methods in Molecular Biology (1986) and Sambrook et al, (supra). Particularly suitable methods include calcium phosphate transfection, DEAE-dextran mediated transfection, transfection, micromjection, cationic lipid-mediated transfection, electroporation, transduction, scrape loading, ballistic introduction or infection (see Sambrook et al, 1989 [supra]; Ausubel et al, 1991 [supra]; Spector, Goldman & Leinwald, 1998). In eukaryotic cells, expression systems may either be transient (for example, episomal) or permanent (chromosomal integration) according to the needs of the system.
• the encoding nucleic acid molecule may or may not include a sequence encoding a control sequence, such as a signal peptide or leader sequence, as desired, for example, for secretion of the translated polypeptide into the lumen of the endoplasmic reticulum, into the periplasmic space or into the extracellular environment.
• a control sequence such as a signal peptide or leader sequence
• These signals may be endogenous to the polypeptide or they may be heterologous signals.
• Leader sequences can be removed by the bacterial host in post- translational processing.
• regulatory sequences that allow for regulation of the expression of the polypeptide relative to the growth of the host cell.
• regulatory sequences are those which cause the expression of a gene to be increased or decreased in response to a chemical or physical stimulus, including the presence of a regulatory compound or to various temperature or metabolic conditions.
• Regulatory sequences are those non-translated regions of the vector, such as enhancers, promoters and 5' and 3' untranslated regions. These interact with host cellular proteins to carry out transcription and translation. Such regulatory sequences may vary in their strength and specificity. Depending on the vector system and host utilised, any number of suitable transcription and translation elements, including constitutive and inducible promoters, may be used.
• inducible promoters such as the hybrid lacZ promoter of the Bluescript phagemid (Stratagene, LaJolla, CA) or pSportlTM plasmid (Gibco BRL) and the like may be used.
• the baculovirus polyhedrin promoter may be used in insect cells. Promoters or enhancers derived from the genomes of plant cells (for example, heat shock, RUBISCO and storage protein genes) or from plant viruses (for example, viral promoters or leader sequences) may be cloned into the vector. In mammalian cell systems, promoters from mammalian genes or from mammalian viruses are preferable. If it is necessary to generate a cell line that contains multiple copies of the sequence, vectors based on SV40 or EBV may be used with an appropriate selectable marker.
• An expression vector is constructed so that the particular nucleic acid coding sequence is located in the vector with the appropriate regulatory sequences, the positioning and orientation of the coding sequence with respect to the regulatory sequences being such that the coding sequence is transcribed under the "control" of the regulatory sequences, i.e., RNA polymerase which binds to the DNA molecule at the control sequences transcribes the coding sequence.
• control i.e., RNA polymerase which binds to the DNA molecule at the control sequences transcribes the coding sequence.
• control sequences and other regulatory sequences may be ligated to the nucleic acid coding sequence prior to insertion into a vector.
• the coding sequence can be cloned directly into an expression vector that already contains the control sequences and an appropriate restriction site.
• cell lines which stably express the polypeptide of interest may be transformed using expression vectors which may contain viral origins of replication and/or endogenous expression elements and a selectable marker gene on the same or on a separate vector. Following the introduction of the vector, cells may be allowed to grow for 1-2 days in an enriched media before they are switched to selective media.
• the pu ⁇ ose of the selectable marker is to confer resistance to selection, and its presence allows growth and recovery of cells that successfully express the introduced sequences.
• Resistant clones of stably transformed cells may be proliferated using tissue culture techniques appropriate to the cell type.
• Mammalian cell lines available as hosts for expression are known in the art and include many immortalised cell lines available from the American Type Culture Collection (ATCC) including, but not limited to, Chinese hamster ovary (CHO), HeLa, baby hamster kidney (BHK), monkey kidney (COS), C127, 3T3, BHK, HEK 293, Bowes melanoma and human hepatocellular carcinoma (for example Hep G2) cells and a number of other cell lines.
• ATCC American Type Culture Collection
• CHO Chinese hamster ovary
• BHK baby hamster kidney
• COS monkey kidney
• C127, 3T3, BHK, HEK 293, Bowes melanoma and human hepatocellular carcinoma (for example Hep G2) cells and a number of other cell lines.
• the materials for baculovirus/insect cell expression systems are commercially available in kit form from, inter alia, Invitrogen, San Diego CA (the "MaxBac" kit).
• host cells include insect cells such as Drosophila S2 and Spodoptera Sf9 cells.
• all plants from which protoplasts can be isolated and cultured to give whole regenerated plants can be utilised, so that whole plants are recovered which contain the transferred gene.
• Practically all plants can be regenerated from cultured cells or tissues, including but not limited to all major species of sugar cane, sugar beet, cotton, fruit and other trees, legumes and vegetables.
• Examples of particularly preferred bacterial host cells include streptococci, staphylococci, E. coli, Streptomyces and Bacillus subtilis cells.
• yeast cells for example, S. cerevisiae
• Aspergillus cells examples include yeast cells (for example, S. cerevisiae) and Aspergillus cells.
• any number of selection systems are known in the art that may be used to recover transformed cell lines. Examples include the he ⁇ es simplex virus thymidine kinase (Wigler, M. et al. (1977) Cell 11:223-32) and adenine phosphoribosyltransferase (Lowy, I. et al. (1980) Cell 22:817-23) genes that can be employed in tk " or aprt* cells, respectively.
• antirnetabolite, antibiotic or herbicide resistance can be used as the basis for selection; for example, dihydrofolate reductase (DHFR) that confers resistance to methotrexate (Wigler, M. et al. (1980) Proc. Natl. Acad. Sci. 77:3567-70); npt, which confers resistance to the aminoglycosides neomycin and G-418 (Colbere-Garapin, F. et al (1981) J. Mol. Biol. 150:1-14) and als or pat, which confer resistance to chlorsulfuron and phosphinotricin acetyltransferase, respectively. Additional selectable genes have been described, examples of which will be clear to those of skill in the art.
• marker gene expression suggests that the gene of interest is also present, its presence and expression may need to be confirmed.
• a marker gene can be placed in tandem with a sequence encoding a polypeptide of the invention under the control of a single promoter. Expression of the marker gene in response to induction or selection usually indicates expression of the tandem gene as well.
• host cells that contain a nucleic acid sequence encoding a polypeptide of the invention and which express said polypeptide may be identified by a variety of procedures known to those of skill in the art. These procedures include, but are not limited to, DNA-DNA or DNA- RNA hybridizations and protein bioassays, for example, fluorescence activated cell sorting (FACS) or immunoassay techniques (such as the enzyme-linked immunosorbent assay [ELISA] and radioimmunoassay [RIA]), that include membrane, solution, or chip based technologies for the detection and/or quantification of nucleic acid or protein (see Hampton, R. et al. (1990) Serological Methods, a Laboratory Manual, APS Press, St Paul, MN) and Maddox, D.E. et al. (1983) J. Exp. Med, 158, 1211-1216).
• FACS fluorescence activated cell sorting
• ELISA enzyme-linked immunosorbent assay
• RIA radioimmunoassay
• Means for producing labelled hybridization or PCR probes for detecting sequences related to nucleic acid molecules encoding polypeptides of the present invention include oligolabelling, nick translation, end-labelling or PCR amplification using a labelled polynucleotide.
• sequences encoding the polypeptide of the invention may be cloned into a vector for the production of an mRNA probe.
• RNA polymerase such as T7, T3 or SP6 and labelled nucleotides. These procedures may be conducted using a variety of commercially available kits (Pharmacia & Upjohn, (Kalamazoo, MI); Promega (Madison WI); and U.S. Biochemical Co ⁇ ., Cleveland, OH)).
• Suitable reporter molecules or labels include radionuclides, enzymes and fluorescent, chermmatinescent or chromogenic agents as well as substrates, cofactors, inhibitors, magnetic particles, and the like.
• Nucleic acid molecules according to the present invention may also be used to create transgenic animals, particularly rodent animals. Such transgenic animals form a further aspect of the present invention. This may be done locally by modification of somatic cells, or by germ line therapy to inco ⁇ orate heritable modifications. Such transgenic animals may be particularly useful in the generation of animal models for drug molecules effective as modulators of the polypeptides of the present invention.
• the polypeptide can be recovered and purified from recombinant cell cultures by well-known methods including ammonium sulphate or ethanol precipitation, acid extraction, anion or cation exchange chromatography, phosphocellulose chromatography, hydrophobic interaction chromatography, affinity chromatography, hydroxylapatite chromatography and lectin chromatography. High performance liquid chromatography is particularly useful for purification. Well known techniques for refolding proteins may be employed to regenerate an active conformation when the polypeptide is denatured during isolation and or purification.
• Specialised vector constructions may also be used to facilitate purification of proteins, as desired, by joining sequences encoding the polypeptides of the invention to a nucleotide sequence encoding a polypeptide domain that will facilitate purification of soluble proteins.
• purification-facilitating domains include metal chelating peptides such as histidine-tryptophan modules that allow purification on immobilised metals, protein A domains that allow purification on immobilised immunoglobulin, and the domain utilised in the FLAGS extension/affinity purification system (Immunex Co ⁇ ., Seattle, WA).
• cleavable linker sequences such as those specific for Factor XA or enterokinase (Invitrogen, San Diego, CA) between the purification domain and the polypeptide of the invention may be used to facilitate purification.
• One such expression vector provides for expression of a fusion protein containing the polypeptide of the invention fused to several histidine residues preceding a thioredoxin or an enterokinase cleavage site.
• the histidine residues facilitate purification by JJVIAC (immobilised metal ion affinity chromatography as described in Porath, J. et al. (1992), Prot. Exp. Purif.
• the polypeptide is to be expressed for use in screening assays, generally it is preferred that it be produced at the surface of the host cell in which it is expressed. In this event, the host cells may be harvested prior to use in the screening assay, for example using techniques such as fluorescence activated cell sorting (FACS) or immunoaffinity techniques. If the polypeptide is secreted into the medium, the medium can be recovered in order to recover and purify the expressed polypeptide. If polypeptide is produced intracellularly, the cells must first be lysed before the polypeptide is recovered.
• FACS fluorescence activated cell sorting
• the polypeptide of the invention can be used to screen libraries of compounds in any of a variety of drug screening techniques. Such compounds may activate (agonise) or inhibit (antagonise) the level of expression of the gene or the activity of the polypeptide of the invention and form a further aspect of the present invention. Preferred compounds are effective to alter the expression of a natural gene which encodes a polypeptide of the second or third aspect of the invention or to regulate the activity of a polypeptide of the second or third aspect of the invention.
• Agonist or antagonist compounds may be isolated from, for example, cells, cell-free preparations, chemical libraries or natural product mixtures. These agonists or antagonists may be natural or modified substrates, ligands, enzymes, receptors or structural or functional mimetics. For a suitable review of such screening techniques, see Coligan et al, Current Protocols in Immunology l(2):Chapter 5 (1991).
• Compounds that are most likely to be good antagonists are molecules that bind to the polypeptide of the invention without inducing the biological effects of the polypeptide upon binding to it.
• Potential antagonists include small organic molecules, peptides, polypeptides and antibodies that bind to the polypeptide of the invention and thereby inhibit or extinguish its activity. In this fashion, binding of the polypeptide to normal cellular binding molecules may be inhibited, such that the normal biological activity of the polypeptide is prevented.
• the polypeptide of the invention that is employed in such a screening technique may be free in solution, affixed to a solid support, borne on a cell surface or located intracellularly.
• screening procedures may involve using appropriate cells or cell membranes that express the polypeptide that are contacted with a test compound to observe binding, or stimulation or inhibition of a functional response.
• the functional response of the cells contacted with the test compound is then compared with control cells that were not contacted with the test compound.
• Such an assay may assess whether the test compound results in a signal generated by activation of the polypeptide, using an appropriate detection system.
• Inhibitors of activation are generally assayed in the presence of a known agonist and the effect on activation by the agonist in the presence of the test compound is observed.
• a preferred method for identifying an agonist or antagonist compound of a polypeptide of the present invention comprises:
• a further preferred method for identifying an agonist or antagonist of a polypeptide of the invention comprises:
• the general methods that are described above may further comprise conducting the identification of agonist or antagonist in the presence of labelled or unlabelled ligand for the polypeptide.
• a compound capable of causing reduction of binding of a ligand is considered to be an agonist or antagonist.
• the ligand is labelled.
• a method of screening for a polypeptide antagonist or agonist compound comprises the steps of:
• step (c) adding a candidate compound to a mixture of labelled ligand and the whole cell or the cell membrane of step (a) and allowing the mixture to attain equilibrium;
• step (d) measuring the amount of labelled ligand bound to the whole cell or the cell membrane after step (c); and (e) comparing the difference in the labelled ligand bound in step (b) and (d), such that the compound which causes the reduction in binding in step (d) is considered to be an agonist or antagonist.
• the INSP123, 1NSP124 and INSP125 polypeptides of the present invention may modulate cellular growth and differentiation.
• the biological activity of the INSP123, INSP124 and INSP125 polypeptides can be examined in systems that allow the study of cellular growth and differentiation such as organ culture assays or in colony assay systems in agarose culture. Stimulation or inhibition of cellular proliferation may be measured by a variety of assays.
• a solid or liquid medium For example, for observing cell growth inhibition, one can use a solid or liquid medium. In a solid medium, cells undergoing growth inhibition can easily be selected from the subject cell group by comparing the sizes of colonies formed. In a liquid medium, growth inhibition can be screened by measuring culture medium turbidity or inco ⁇ oration of labelled thymidine in DNA. Typically, the inco ⁇ oration of a nucleoside analog into newly synthesised DNA may be employed to measure proliferation (i. e., active cell growth) in a population of cells. For example, bromodeoxyuridine (BrdU) can be employed as a DNA labelling reagent and anti-BrdU mouse monoclonal antibodies can be employed as a detection reagent.
• bromodeoxyuridine BrdU
• anti-BrdU mouse monoclonal antibodies can be employed as a detection reagent.
• This antibody binds only to cells containing DNA which has inco ⁇ orated bromodeoxyuridine.
• detection methods may be used in conjunction with this assay including immunofluorescence, immunohistochemical, ELISA, and colorimetric methods. Kits that include bromodeoxyuridine (BrdU) and anti-BrdU mouse monoclonal antibody are commercially available from Boehringer Mannheim (Indianapolis, EN).
• the effect of the JNSP123, INSP124 and P SP125 polypeptides upon cellular differentiation can be measured by contacting stem cells or embryonic cells with various amounts of the INSP123, INSP124 and INSP125 polypeptides and observing the effect upon differentiation of the stem cells or embryonic cells. Tissue-specific antibodies and microscopy may be used to identify the resulting cells.
• the INSP123, JNSP124 and EMSP125 polypeptides may also be found to modulate immune and/or nervous system cell proliferation and differentiation in a dose-dependent manner in the above-described assays.
• the "functional equivalents" of the INSP123, INSP124, and INSP125 polypeptides include polypeptides that exhibit any of the same growth and differentiation regulating activities in the above-described assays in a dose-dependent manner.
• the degree of dose-dependent activity need not be identical to that of the INSP123, INSP124 and INSP125 polypeptides, preferably the "functional equivalents" will exhibit substantially similar dose-dependence in a given activity assay compared to the INSP123, ESTSP124 and JNSP125 polypeptides.
• simple binding assays may be used, in which the adherence of a test compound to a surface bearing the polypeptide is detected by means of a label directly or indirectly associated with the test compound or in an assay involving competition with a labelled competitor.
• competitive drug screening assays may be used, in which neutralising antibodies that are capable of binding the polypeptide specifically compete with a test compound for binding. In this manner, the antibodies can be used to detect the presence of any test compound that possesses specific binding affinity for the polypeptide.
• Assays may also be designed to detect the effect of added test compounds on the production of mRNA encoding the polypeptide in cells.
• an ELISA may be constructed that measures secreted or cell-associated levels of polypeptide using monoclonal or polyclonal antibodies by standard methods known in the art, and this can be used to search for compounds that may inhibit or enhance the production of the polypeptide from suitably manipulated cells or tissues. The formation of binding complexes between the polypeptide and the compound being tested may then be measured.
• Another technique for drug screening which may be used provides for high throughput screening of compounds having suitable binding affinity to the polypeptide of interest (see International patent application WO84/03564).
• This method large numbers of different small test compounds are synthesised on a solid substrate, which may then be reacted with the polypeptide of the invention and washed.
• One way of immobilising the polypeptide is to use non-neutralising antibodies. Bound polypeptide may then be detected using methods that are well known in the art. Purified polypeptide can also be coated directly onto plates for use in the aforementioned drug screening techniques.
• the polypeptide of the invention may be used to identify membrane-bound or soluble receptors, through standard receptor binding techniques that are known in the art, such as ligand binding and crosslinking assays in which the polypeptide is labelled with a radioactive isotope, is chemically modified, or is fused to a peptide sequence that facilitates its detection or purification, and incubated with a source of the putative receptor (for example, a composition of cells, cell membranes, cell supernatants, tissue extracts, or bodily fluids).
• a source of the putative receptor for example, a composition of cells, cell membranes, cell supernatants, tissue extracts, or bodily fluids.
• the efficacy of binding may be measured using biophysical techniques such as surface plasmon resonance and spectroscopy.
• Binding assays may be used for the purification and cloning of the receptor, but may also identify agonists and antagonists of the polypeptide, that compete with the binding of the polypeptide to its receptor. Standard methods for conducting screening assays are well understood in the art.
• the invention also includes a screening kit useful in the methods for identifying agonists, antagonists, ligands, receptors, substrates, enzymes, that are described above.
• the invention includes the agonists, antagonists, ligands, receptors, substrates and enzymes, and other compounds which modulate the activity or antigenicity of the polypeptide of the invention discovered by the methods that are described above.
• compositions comprising a polypeptide, nucleic acid, ligand or compound of the invention in combination with a suitable pharmaceutical carrier.
• suitable pharmaceutical carrier may be suitable as therapeutic or diagnostic reagents, as vaccines, or as other immunogenic compositions, as outlined in detail below.
• a composition containing a polypeptide, nucleic acid, ligand or compound [X] is "substantially free of impurities [herein, Y] when at least 85% by weight of the total X+Y in the composition is X.
• X comprises at least about 90% by weight of the total of X+Y in the composition, more preferably at least about 95%, 98% or even 99% by weight.
• compositions should preferably comprise a therapeutically effective amount of the polypeptide, nucleic acid molecule, ligand, or compound of the invention.
• therapeutically effective amount refers to an amount of a therapeutic agent needed to treat, ameliorate, or prevent a targeted disease or condition, or to exhibit a detectable therapeutic or preventative effect.
• the therapeutically effective dose can be estimated initially either in cell culture assays, for example, of neoplastic cells, or in animal models, usually mice, rabbits, dogs, or pigs. The animal model may also be used to determine the appropriate concentration range and route of administration. Such information can then be used to determine useful doses and routes for administration in humans.
• an effective amount for a human subject will depend upon the severity of the disease state, general health of the subject, age, weight, and gender of the subject, diet, time and frequency of administration, drug combination(s), reaction sensitivities, and tolerance/response to therapy. This amount can be determined by routine experimentation and is within the judgement of the clinician. Generally, an effective dose will be from 0.01 mg/kg to 50 mg/kg, preferably 0.05 mg/kg to 10 mg/kg. Compositions may be administered individually to a patient or may be administered in combination with other agents, drugs or hormones.
• a pharmaceutical composition may also contain a pharmaceutically acceptable carrier, for administration of a therapeutic agent.
• a pharmaceutically acceptable carrier for administration of a therapeutic agent.
• Such carriers include antibodies and other polypeptides, genes and other therapeutic agents such as liposomes, provided that the carrier does not itself induce the production of antibodies harmful to the individual receiving the composition, and which may be administered without undue toxicity.
• Suitable carriers may be large, slowly metabolised macromolecules such as proteins, polysaccharides, polylactic acids, polyglycolic acids, polymeric amino acids, amino acid copolymers and inactive virus particles.
• Pharmaceutically acceptable salts can be used therein, for example, mineral acid salts such as hydrochlorides, hydrobromides, phosphates, sulphates, and the like; and the salts of organic acids such as acetates, propionates, malonates, benzoates, and the like.
• mineral acid salts such as hydrochlorides, hydrobromides, phosphates, sulphates, and the like
• organic acids such as acetates, propionates, malonates, benzoates, and the like.
• Pharmaceutically acceptable carriers in therapeutic compositions may additionally contain liquids such as water, saline, glycerol and ethanol. Additionally, auxiliary substances, such as wetting or emulsifying agents, pH buffering substances, and the like, may be present in such compositions. Such carriers enable the pharmaceutical compositions to be formulated as tablets, pills, dragees, capsules, liquids, gels, syrups, slurries, suspensions, and the like, for ingestion by the patient.
• compositions of the invention can be administered directly to the subject.
• the subjects to be treated can be animals; in particular, human subjects can be treated.
• compositions utilised in this invention may be administered by any number of routes including, but not limited to, oral, intravenous, intramuscular, intra-arterial, intrarnedullary, intrathecal, intraventricular, transdermal or transcutaneous applications (for example, see WO98/20734), subcutaneous, intraperitoneal, intranasal, enteral, topical, sublingual, intravaginal or rectal means.
• Gene guns or hyposprays may also be used to administer the pharmaceutical compositions of the invention.
• the therapeutic compositions may be prepared as injectables, either as liquid solutions or suspensions; solid forms suitable for solution in, or suspension in, liquid vehicles prior to injection may also be prepared.
• Direct delivery of the compositions will generally be accomplished by injection, subcutaneously, intraperitoneally, intravenously or intramuscularly, or delivered to the interstitial space of a tissue.
• the compositions can also be administered into a lesion. Dosage treatment may be a single dose schedule or a multiple dose schedule.
• One approach comprises administering to a subject an inhibitor compound (antagonist) as described above, along with a pharmaceutically acceptable carrier in an amount effective to inhibit the function of the polypeptide, such as by blocking the binding of ligands, substrates, enzymes, receptors, or by inhibiting a second signal, and thereby alleviating the abnormal condition.
• an inhibitor compound as described above
• a pharmaceutically acceptable carrier in an amount effective to inhibit the function of the polypeptide, such as by blocking the binding of ligands, substrates, enzymes, receptors, or by inhibiting a second signal, and thereby alleviating the abnormal condition.
• antagonists are antibodies.
• such antibodies are chimeric and/or humanised to minimise their immunogenicity, as described previously.
• polypeptide that retain binding affinity for the ligand, substrate, enzyme, receptor, in question, may be administered.
• polypeptide may be administered in the form of fragments that retain the relevant portions.
• expression of the gene encoding the polypeptide can be inhibited using expression-blocking techniques, such as the use of antisense nucleic acid molecules (as described above), either internally generated or separately administered.
• Modifications of gene expression can be obtained by designing complementary sequences or antisense molecules (DNA, RNA, or PNA) to the control, 5' or regulatory regions (signal sequence, promoters, enhancers and introns) of the gene encoding the polypeptide.
• inhibition can be achieved using "triple helix" base- pairing methodology. Triple helix pairing is useful because it causes inhibition of the ability of the double helix to open sufficiently for the binding of polymerases, transcription factors, or regulatory molecules.
• the complementary sequence or antisense molecule may also be designed to block translation of mRNA by preventing the transcript from binding to ribosomes.
• Such oligonucleotides may be administered or may be generated in situ from expression in vivo.
• Ribozymes are catalytically active RNAs that can be natural or synthetic (see for example Usman, N, et al, Curr. Opin. Struct. Biol (1996) 6(4), 527- 33). Synthetic ribozymes can be designed to specifically cleave mRNAs at selected positions thereby preventing translation of the mRNAs into functional polypeptide. Ribozymes may be synthesised with a natural ribose phosphate backbone and natural bases, as normally found in RNA molecules. Alternatively the ribozymes may be synthesised with non-natural backbones, for example, 2'-0-methyl RNA, to provide protection from ribonuclease degradation and may contain modified bases.
• RNA molecules may be modified to increase intracellular stability and half-life. Possible modifications include, but are not limited to, the addition of flanking sequences at the 5' and/or 3' ends of the molecule or the use of phosphorothioate or 2' O-methyl rather than phosphodiesterase linkages within the backbone of the molecule. This concept is inherent in the production of PNAs and can be extended in all of these molecules by the inclusion of non-traditional bases such as inosine, queosine and butosine, as well as acetyl-, methyl-, thio- and similarly modified forms of adenine, cytidine, guanine, thymine and uridine which are not as easily recognised by endogenous endonucleases.
• One approach comprises administering to a subject a therapeutically effective amount of a compound that activates the polypeptide, i.e., an agonist as described above, to alleviate the abnormal condition.
• a therapeutic amount of the polypeptide in combination with a suitable pharmaceutical carrier may be administered to restore the relevant physiological balance of polypeptide.
• Gene therapy may be employed to effect the endogenous production of the polypeptide by the relevant cells in the subject. Gene therapy is used to treat permanently the inappropriate production of the polypeptide by replacing a defective gene with a corrected therapeutic gene.
• Gene therapy of the present invention can occur in vivo or ex vivo.
• Ex vivo gene therapy requires the isolation and purification of patient cells, the introduction of a therapeutic gene and introduction of the genetically altered cells back into the patient.
• in vivo gene therapy does not require isolation and purification of a patient's cells.
• the therapeutic gene is typically "packaged" for administration to a patient.
• Gene delivery vehicles may be non-viral, such as liposomes, or replication-deficient viruses, such as adenovirus as described by Berkner, K.L., in Curr. Top. Microbiol. Immunol., 158, 39-66 (1992) or adeno- associated virus (AAV) vectors as described by Muzyczka, N., in Curr. Top. Microbiol. Immunol., 158, 97-129 (1992) and U.S. Patent No. 5,252,479.
• a nucleic acid molecule encoding a polypeptide of the invention may be engineered for expression in a replication-defective retroviral vector.
• This expression construct may then be isolated and introduced into a packaging cell transduced with a retroviral plasmid vector containing RNA encoding the polypeptide, such that the packaging cell now produces infectious viral particles containing the gene of interest.
• These producer cells may be administered to a subject for engineering cells in vivo and expression of the polypeptide in vivo (see Chapter 20, Gene Therapy and other Molecular Genetic-based Therapeutic Approaches, (and references cited therein) in Human Molecular Genetics (1996), T Strachan and A P Read, BIOS Scientific Publishers Ltd).
• Another approach is the administration of "naked DNA" in which the therapeutic gene is directly injected into the bloodstream or muscle tissue.
• the invention provides that they can be used in vaccines to raise antibodies against the disease causing agent.
• Vaccines according to the invention may either be prophylactic (i.e. to prevent infection) or therapeutic (i.e. to treat disease after infection).
• Such vaccines comprise immunising antigen(s), immunogen(s), polypeptide(s), protein(s) or nucleic acid, usually in combination with pharmaceutically-acceptable carriers as described above, which include any carrier that does not itself induce the production of antibodies ha ⁇ nful to the individual receiving the composition. Additionally, these carriers may function as immunostimulating agents ("adjuvants").
• the antigen or immunogen may be conjugated to a bacterial toxoid, such as a toxoid from diphtheria, tetanus, cholera, H. pylori, and other pathogens.
• vaccines comprising polypeptides are preferably administered parenterally (for instance, subcutaneous, intramuscular, intravenous, or intradermal injection).
• parenteral administration include aqueous and non-aqueous sterile injection solutions which may contain anti-oxidants, buffers, bacteriostats and solutes which render the formulation isotonic with the blood of the recipient, and aqueous and non- aqueous sterile suspensions which may include suspending agents or thickening agents.
• the vaccine formulations of the invention may be presented in unit-dose or multi-dose containers.
• sealed ampoules and vials and may be stored in a freeze-dried condition requiring only the addition of the sterile liquid carrier immediately prior to use.
• the dosage will depend on the specific activity of the vaccine and can be readily determined by routine experimentation.
• This invention also relates to the use of nucleic acid molecules according to the present invention as diagnostic reagents. Detection of a mutated form of the gene characterised by the nucleic acid molecules of the invention which is associated with a dysfunction will provide a diagnostic tool that can add to, or define, a diagnosis of a disease, or susceptibility to a disease, which results from under-expression, over-expression or altered spatial or temporal expression of the gene. Individuals carrying mutations in the gene may be detected at the DNA level by a variety of techniques.
• Nucleic acid molecules for diagnosis may be obtained from a subject's cells, such as from blood, urine, saliva, tissue biopsy or autopsy material.
• the genomic DNA may be used directly for detection or may be amplified enzymatically by using PCR, ligase chain reaction (LCR), strand displacement amplification (SDA), or other amplification techniques (see Saiki et al, Nature, 324, 163-166 (1986); Bej, et al, Crit. Rev. Biochem. Molec. Biol., 26, 301-334 (1991); Birkenmeyer et al, J. Virol. Meth., 35, 117-126 (1991); Van Brunt, J., Bio/Technology, 8, 291-294 (1990)) prior to analysis.
• LCR ligase chain reaction
• SDA strand displacement amplification
• this aspect of the invention provides a method of diagnosing a disease in a patient, comprising assessing the level of expression of a natural gene encoding a polypeptide according to the invention and comparing said level of expression to a control level, wherein a level that is different to said control level is indicative of disease.
• the method may comprise the steps of:
• step b) contacting a control sample with said probe under the same conditions used in step a);
• a further aspect of the invention comprises a diagnostic method comprising the steps of:
• an amplification step for example using PCR, may be included.
• Deletions and insertions can be detected by a change in the size of the amplified product in comparison to the normal genotype.
• Point mutations can be identified by hybridizing amplified DNA to labelled RNA of the invention or alternatively, labelled antisense DNA sequences of the invention. Perfectly-matched sequences can be distinguished from mismatched duplexes by RNase digestion or by assessing differences in melting temperatures.
• the presence or absence of the mutation in the patient may be detected by contacting DNA with a nucleic acid probe that hybridises to the DNA under stringent conditions to form a hybrid double-stranded molecule, the hybrid double-stranded molecule having an unhybridised portion of the nucleic acid probe strand at any portion corresponding to a mutation associated with disease; and detecting the presence or absence of an unhybridised portion of the probe strand as an indication of the presence or absence of a disease-associated mutation in the corresponding portion of the DNA strand.
• Point mutations and other sequence differences between the reference gene and "mutant" genes can be identified by other well-known techniques, such as direct DNA sequencing or single-strand conformational polymo ⁇ hism, (see Orita et al, Genomics, 5, 874-879 (1989)).
• a sequencing primer may be used with double-stranded PCR product or a single-stranded template molecule generated by a modified PCR.
• the sequence determination is performed by conventional procedures with radiolabelled nucleotides or by automatic sequencing procedures with fluorescent- tags.
• Cloned DNA segments may also be used as probes to detect specific DNA segments. The sensitivity of this method is greatly enhanced when combined with PCR.
• point mutations and other sequence variations can be detected as described above, for example, through the use of allele-specific oligonucleotides for PCR amplification of sequences that differ by single nucleotides.
• DNA sequence differences may also be detected by alterations in the electrophoretic mobility of DNA fragments in gels, with or without denaturing agents, or by direct DNA sequencing (for example, Myers et al, Science (1985) 230:1242). Sequence changes at specific locations may also be revealed by nuclease protection assays, such as RNase and SI protection or the chemical cleavage method (see Cotton et al, Proc. Natl. Acad. Sci. USA (1985) 85: 4397-4401).
• mutations such as microdeletions, aneuploidies, translocations, inversions, can also be detected by in situ analysis (see, for example, Keller et al, DNA Probes, 2nd Ed., Stockton Press, New York, N.Y., USA (1993)), that is, DNA or RNA sequences in cells can be analysed for mutations without need for their isolation and/or immobilisation onto a membrane.
• Fluorescence in situ hybridization is presently the most commonly applied method and numerous reviews of FISH have appeared (see, for example, Trachuck et al, Science, 250, 559-562 (1990), and Trask et al, Trends, Genet., 7, 149-154 (1991)).
• an array of oligonucleotide probes comprising a nucleic acid molecule according to the invention can be constructed to conduct efficient screening of genetic variants, mutations and polymo ⁇ hisms.
• Array technology methods are well known and have general applicability and can be used to address a variety of questions in molecular genetics including gene expression, genetic linkage, and genetic variability (see for example: M.Chee et al, Science (1996), Vol 274, pp 610-613).
• the array is prepared and used according to the methods described in PCT application W095/11995 (Chee et al); Lockhart, D. J. et al. (1996) Nat. Biotech. 14: 1675-1680); and Schena, M. et al (1996) Proc. Natl. Acad. Sci. 93: 10614-10619).
• Oligonucleotide pairs may range from two to over one million.
• the oligomers are synthesized at designated areas on a substrate using a light-directed chemical process.
• the substrate may be paper, nylon or other type of membrane, filter, chip, glass slide or any other suitable solid support.
• an oligonucleotide may be synthesized on the surface of the substrate by using a chemical coupling procedure and an ink jet application apparatus, as described in PCT application W095/25116 (Baldeschweiler et al).
• a "gridded" array analogous to a dot (or slot) blot may be used to arrange and link cDNA fragments or oligonucleotides to the surface of a substrate using a vacuum system, thermal, UV, mechanical or chemical bonding procedures.
• An array such as those described above, may be produced by hand or by using available devices (slot blot or dot blot apparatus), materials (any suitable solid support), and machines (including robotic instruments), and may contain 8, 24, 96, 384, 1536 or 6144 oligonucleotides, or any other number between two and over one million which lends itself to the efficient use of commercially-available instrumentation.
• diseases may be diagnosed by methods comprising determining, from a sample derived from a subject, an abnormally decreased or increased level of polypeptide or mRNA. Decreased or increased expression can be measured at the RNA level using any of the methods well known in the art for the quantitation of polynucleotides, such as, for example, nucleic acid amplification, for instance PCR, RT-PCR, RNase protection, Northern blotting and other hybridization methods.
• nucleic acid amplification for instance PCR, RT-PCR, RNase protection, Northern blotting and other hybridization methods.
• Assay techniques that can be used to determine levels of a polypeptide of the present invention in a sample derived from a host are well-known to those of skill in the art and are discussed in some detail above (including radioimmunoassays, competitive-binding assays, Western Blot analysis and ELISA assays).
• This aspect of the invention provides a diagnostic method which comprises the steps of: (a) contacting a ligand as described above with a biological sample under conditions suitable for the formation of a ligand-polypeptide complex; and (b) detecting said complex.
• Protocols such as ELISA, RIA, and FACS for measuring polypeptide levels may additionally provide a basis for diagnosing altered or abnormal levels of polypeptide expression.
• Normal or standard values for polypeptide expression are established by combining body fluids or cell extracts taken from normal mammalian subjects, preferably humans, with antibody to the polypeptide under conditions suitable for complex formation The amount of standard complex formation may be quantified by various methods, such as by photometric means.
• Antibodies which specifically bind to a polypeptide of the invention may be used for the diagnosis of conditions or diseases characterised by expression of the polypeptide, or in assays to monitor patients being treated with the polypeptides, nucleic acid molecules, ligands and other compounds of the invention.
• Antibodies useful for diagnostic pu ⁇ oses may be prepared in the same manner as those described above for therapeutics. Diagnostic assays for the polypeptide include methods that utilise the antibody and a label to detect the polypeptide in human body fluids or extracts of cells or tissues.
• the antibodies may be used with or without modification, and may be labelled by joining them, either covalently or non-covalently, with a reporter molecule.
• a wide variety of reporter molecules known in the art may be used, several of which are described above.
• Diagnostic assays may be used to distinguish between absence, presence, and excess expression of polypeptide and to monitor regulation of polypeptide levels during therapeutic intervention. Such assays may also be used to evaluate the efficacy of a particular therapeutic treatment regimen in animal studies, in clinical trials or in monitoring the treatment of an individual patient.
• a diagnostic kit of the present invention may comprise:
• a diagnostic kit may comprise a first container containing a nucleic acid probe that hybridises under stringent conditions with a nucleic acid molecule according to the invention; a second container containing primers useful for amplifying the nucleic acid molecule; and instructions for using the probe and primers for facilitating the diagnosis of disease.
• the kit may further comprise a third container holding an agent for digesting unhybridised RNA.
• a diagnostic kit may comprise an array of nucleic acid molecules, at least one of which may be a nucleic acid molecule according to the invention.
• a diagnostic kit may comprise one or more antibodies that bind to a polypeptide according to the invention; and a reagent useful for the detection of a binding reaction between the antibody and the polypeptide.
• kits will be of use in diagnosing a disease or susceptibility to disease in members of the vWFC domain containing protein family are implicated.
• diseases may include cell proliferative disorders, including neoplasm, melanoma, lung, colorectal, breast, pancreas, head and neck and other solid tumours; myeloproliferative disorders, such as leukemia, non-Hodgkin lymphoma, leukopenia, thrombocytopenia, angiogenesis disorder, Kaposis' sarcoma; autoimmune/inflammatory disorders, including allergy, inflammatory bowel disease, arthritis, psoriasis and respiratory tract inflammation, asthma, and organ transplant rejection; cardiovascular disorders, including hypertension, oedema, angina, atherosclerosis, thrombosis, sepsis, shock, reperfusion injury, and ischemia; neurological disorders including central nervous system disease, Alzheimer's disease, brain injury, amyotrophic lateral sclerosis, and pain; developmental disorders such as those relating to
• FIG. 1 Alignment of the SECFAM3 family.
• Von Willebrand Factor type C (vWFC) domain 1 spans the region 155-214aa of the alignment and vWFC domain 2 spans the region 221-281aa.
• vWFC Von Willebrand Factor type C
• Figure 2 INSP123, 124 and 125 were all predicted to be secreted proteins based on the prediction of a signal peptide common to all three isoforms ( Figure 2).
• Figure 3 Splicing patterns predicted for the coding exons of this gene (not to scale). INSP123 and INSP125 were based on mouse and macaque cDNA sequences, while INSP124 was a predicted possible splicing pattern that inco ⁇ orated both von Willebrand Factor type C domains. The effect that this splicing had at the sequence level may be seen in Figure 1.
• Figure 4 Alignment of EMSP124 predicted domain 1 and domain 2 (highlighted) against characterized von Willebrand Factor type C domains from a variety of proteins. Darker shading indicates greater sequence conservation.
• Figure 5 Position-specific probability matrix profile of the family based on EMSP124.
• Figure 6 Family consensus sequence in PROSITE format based on INSP124 amino acids 53 to
• Figure 7 Nucleotide sequence of INSP123 prediction with translation.
• Figure 8 Nucleotide sequence with translation of TNSP123 PCR product cloned using primers JNSP123-CPl and INSP123-CP2.
• Figure 9 Map of pCR4-TOPO-JNSP123.
• FIG. 10 Map of pDONR 221.
• Figure 11 Map of expression vector pEAKl 2d.
• Figure 12 Map of Expression vector pDEST12.2.
• Figure 13 Map of pENTR-INSP123-6HIS.
• Figure 14 Map of pEAK12d-INSP123-6HIS.
• Figure 15 Map of pDEST12.2-INSP123-6HIS.
• Figure 16 Nucleotide sequence of INSP124 prediction with translation of the coding sequence.
• Figure 17 INSP124 coding exon organization in genomic DNA and position of PCR primers.
• Figure 18 Nucleotide sequence of cloned INSP124 product with translation of the ORF.
• Figure 19 Map of pCR-BluntII-TOPO-JNSP124.
• FIG. 20 Map of pDONR 221.
• Figure 21 Map of Expression vector pEAK12d.
• Figure 22 Map of Expression vector pDEST12.2.
• Figure 23 Map of pENTR NSP124-6HIS.
• Figure 24 Map of pEAK12d_INSP124-6HIS.
• Figure 25 Map of pDEST12.2_ JNSP124-6HIS.
• Figure 26 Nucleotide sequence of INSP125 prediction with translation of the coding sequence
• Figure 27 INSP125 coding exon organization in genomic DNA and position of PCR primers.
• Figure 28 Nucleotide sequence of cloned INSP125 product with translation of the ORF.
• Figure 29 Map of pCR4-TOPO-INSP125.
• FIG. 30 Map of pDONR 221.
• Figure 31 Map of Expression vector pEAK12d.
• Figure 32 Map of Expression vector pDEST12.2.
• Figure 33 Map of pENTR_JNSP125-6HIS.
• Figure 34 Map of pEAK12d_ENSP125-6HIS.
• Figure 35 Map of pDEST12.2_ JNSP125-6HIS.
• INSP123, INSP124 and ENSP125 have no publicly available annotation, contain a strong secretory protein signature in the form of a signal peptide, and can be clustered with similar proteins such as orthologues from other animal species.
• Table 1 All of the sequences of the SECFAM3 family -with peptide length and, where possible, tissue distribution information included.
• INSP123 SEQ ID NO:2
• INSP124 SEQ JD NO:6
• INSP125 SEQ ED NO:26
• NCBI public or patent databases
• No human cDNA encoding any of these three proteins has yet been identified.
• close homology to macaque and mouse cDNA sequences offers strong supporting evidence that the three INSP sequences disclosed are the human equivalent of the macaque and mouse sequences.
• INSP125 63% ED overall. Split into two regions of 100% ED (Query l-33aa, Target l-33aa, and Query 34-83aa, Target 81-130aa)
• AK083856.1 (Mus musculus 12 days embryo spinal ganglion cDNA, RJKEN full-length enriched library, clone:D130026K08 productihypothetical von Willebrand factor, type C repeat containing protein, full insert sequence.)
• G 873 An extra G nucleotide (G 873) introduced a frame-shift in this sequence which was not supported by the genomic DNA for that region.
• INSP124: 99% ED, Query l-130aa, Target l-130aa, e le-78.
• AK080585.1 (Mus musculus 10 days neonate cortex cDNA, RIKEN full-length enriched library, product hypothetical von Willebrand factor, type C repeat containing protein, full insert sequence.) The statistics for the translated product are shown below:
• INSP123 63% ID overall. Splits into two regions of 100% ED (Query 1-33, Target 1-33, and
• INSP124 77% ID overall. Splits into two regions of 100% and 98%> ED respectively (Query 1- 33aa, Target l-33aa, and Query 81-222aa, Target 34-175aa).
• the SignalP program http://www.cbs.dtu.dk/services/SignalP/ was used to identify the potential signal peptide regions and cleavage sites for the INSP123-125 polypeptides. Since these three polypeptides share the same initial sequence, the SignalP results were identical for the three isoforms, that is, the SignalP results for INSP123 (SEQ ED NO:2), INSP124 (SEQ JD NO:12) and INSP125 (SEQ ED NO:26) all indicate that the cleavage site is most likely to be between positions 23 and 24 ( Figure 2).
• Example 4 Evidence for the presence of a vWFC domain within the SECFAM3 family
• INSP123 contains only domain 1 (53-109aa of SEQ ID NO:2), whereas JNSP124 contains both domains (53-109aa and 116-171aa of SEQ ED NO:12).
• Isoform INSP125 (SEQ ID NO:26) is characterised in that there is a region spliced between positions 136 and 182 in the alignment ( Figures 1 and 3). This effectively deletes the first four cysteines of domain 1, most likely rendering domain 1 non-functional as a vWFC domain. Domain 2, however, is not corrupted by this splicing event and consequently represents the single vWFC domain seen in this protein (69- 124aa of SEQ ED NO:26).
• Splice variants of the polypeptides of the invention are predicted to have different biological functions, such as possessing different affinities for binding partners.
• Figure 5 shows the position-specific score matrix, or profile, for the SECFAM3 family. This represents the unique signature of the family.
• the profile was generated by first creating a multiple alignment of the sequences. A template sequence was chosen, in this case INSP124, to construct a profile around. The frequency of each of the possible 20 amino acid types was assessed for each column of the family multiple sequence alignment that was occupied by a residue of the template sequence. The score of each amino acid residue type at each position in the family alignment was calculated based on the frequency scores and the likelihood of seeing a substitution of the dominant residue with this residue type, based on the BLOSUM62 position-independent background matrix (Henikoff & Henikoff, 1992. Proc. Natl. Acad. Sci. USA, 89:10915-9).
• This matrix is based on a large dataset of family alignment blocks (BLOcks Substitution Matrix) where amino acid substitution frequencies were assessed based on alignments clustered at 62% identity or greater. In this case, these factors were pooled to give a logarithm-based score for each amino acid type at each position in the SECFAM3 alignment. The highest positive scores represent those amino acids that are most likely to be found at that position.
• This profile can be used to find an alignment score of a query sequence. At each position, the corresponding value for that amino acid is extracted and the sum of all such scores for each amino acid of the query sequence constitutes the alignment score for that sequence. If this is above a certain threshold value, the query sequence may be significantly related to the family. The profile, then, forms a sensitive statistical standard for the family. BLASTP of INSP124 against itself yields a minimum E-value of e- 143.
• Example 7 Generating a consensus sequence in PROSITE format for the SECFAM3 family
• Figure 6 shows a consensus sequence that represents the first domain of the proteins in the SECFAM3 family.
• the domain is predicted to be a vWFC domain.
• the second domain is also annotated as a vWFC domain.
• First strand cDNA was prepared from a variety of normal human tissue total RNA samples (purchased from Clontech, Stratagene, Ambion, Biochain Institute and prepared in-house) using Superscript II RNase H " Reverse Transcriptase (Invitrogen) according to the manufacturer's protocol.
• the contents of the tube were collected by brief centrifugation and 4 ⁇ l of 5X First-Strand Buffer, 2 ⁇ l 0.1 M DTT, and 1 ⁇ l RnaseOUT Recombinant Ribonuclease Inhibitor (40 units/ ⁇ l, Invitrogen) were added.
• the contents of the tube were mixed gently and incubated at 42 °C for 2 min; then 1 ⁇ l (200 units) of Superscript II enzyme was added and mixed gently by pipeting. The mixture was incubated at 42 °C for 50 min and then inactivated by heating at 70 °C for 15 min.
• 1 ⁇ l (2 units) of E 1 ⁇ l (2 units) of E.
• coli RNase H (Invitrogen) was added and the reaction mixture incubated at 37 °C for 20 min. The final 21 ⁇ l of reaction mix was diluted by adding 179 ⁇ l sterile water to give a total volume of 200 ⁇ l.
• the human cDNA sample used as a template for the amplification of INSP123 was derived from brain. cDNA libraries
• Human cDNA libraries (in bacteriophage lambda ( ⁇ ) vectors) were purchased from Clontech, Invitrogen, or made in-house in ⁇ GT10 vectors. Bacteriophage ⁇ DNA was prepared from small scale cultures of infected E.coli host strain using the Wizard Lambda Preps DNA purification system according to the manufacturer's instructions (Promega, Co ⁇ oration, Madison WI). Human cDNA library samples used as templates for the amplification of INSP123 were derived from fetal brain, adult brain, and a mixed brain-lung-testis library.
• PCR primers having a length of between 18 and 25 bases were designed for amplifying the complete coding sequence of the virtual cDNA using Primer Designer Software (Scientific & Educational Software, PO Box 72045, Durham, NC 27722-2045, USA). PCR primers were optimized to have a Tm close to 55 + 10 °C and a GC content of 40-60%. Primers were selected which had high selectivity for the target sequence (INSP123) with little or no non-specific priming.
• Gene-specific cloning primers (INSP123-CP1 and JNSP123-CP2, Figure 7, Figure 8 and Table 1) were designed to amplify a cDNA fragment of 482 bp covering the entire 414 bp coding sequence of the INSP123 prediction. Interrogation of public EST sequence databases with the INSP123 prediction suggested that the sequence might be expressed in brain cDNA templates.
• the gene-specific cloning primers EMSP123-CP1 and TNSP123-CP2 were therefore used with a human cDNA sample from brain and the phage library cDNA samples listed in Section 1.2 as the PCR templates.
• the PCR was performed in a final volume of 50 ⁇ l containing IX AmpliTaqTM buffer, 200 ⁇ M dNTPs, 50 pmoles of each cloning primer, 2.5 units of AmpliTaqTM (Perkin Elmer) and 100 ng of cDNA template using an MJ Research DNA Engine, programmed as follows: 94 °C, 2 min; 40 cycles of 94 °C, 1 min, 53 °C, 1 min, and 72 °C, 1 min; followed by 1 cycle at 72 °C for 7 min and a holding cycle at 4 °C.
• reaction mixture (50 ⁇ l) of each amplification was analysed on a 0.8 % agarose gel in 1 X
• TAE buffer Invitrogen
• a single PCR product was seen migrating at approximately the predicted molecular mass in the sample corresponding to the brain-lung-testis cDNA library template.
• This PCR product was purified using the Wizard PCR Preps DNA Purification System (Promega). The PCR product was eluted in 50 ⁇ l of water and subcloned directly.
• the PCR product was subcloned into the topoisomerase I modified cloning vector (pCR4-TOPO) using the TA cloning kit purchased from the Invitrogen Co ⁇ oration using the conditions specified by the manufacturer. Briefly, 4 ⁇ l of gel purified PCR product from the brain-lung-testis cDNA library amplification was incubated for 15 min at room temperature with 1 ⁇ l of TOPO vector and 1 ⁇ l salt solution. The reaction mixture was then transformed into E. coli strain TOP10 (Invitrogen) as follows: a 50 ⁇ l aliquot of One Shot TOP10 cells was thawed on ice and 2 ⁇ l of TOPO reaction was added.
• E. coli strain TOP10 Invitrogen
• the mixture was incubated for 15 min on ice and then heat shocked by incubation at 42 °C for exactly 30 s. Samples were returned to ice and 250 ⁇ l of warm (room temperature) SOC media was added. Samples were incubated with shaking (220 ⁇ m) for 1 h at 37 °C. The transformation mixture was then plated on L-broth (LB) plates containing ampicillin (100 ⁇ g/ml) and incubated overnight at 37 °C.
• LB L-broth
• Colonies were inoculated into 50 ⁇ l sterile water using a sterile toothpick. A 10 ⁇ l aliquot of the inoculum was then subjected to PCR in a total reaction volume of 20 ⁇ l containing I AmpliTaqTM buffer, 200 ⁇ M dNTPs, 20 pmoles T7 primer, 20 pmoles of T3 primer, 1 unit of AmpliTaqTM (Perkin Elmer) using an MJ Research DNA Engine. The cycling conditions were as follows: 94 °C, 2 min; 30 cycles of 94 °C, 30 sec, 48 °C, 30 sec and 72 °C for 1 min. Samples were maintained at 4 °C (holding cycle) before further analysis.
• PCR reaction products were analyzed on 1 % agarose gels in 1 X TAE buffer. Colonies which gave the expected PCR product size (482 bp cDNA + 105 bp due to the multiple cloning site or MCS) were grown up overnight at 37 °C in 5 ml L-Broth (LB) containing ampicillin (100 ⁇ g /ml), with shaking at 220 ⁇ m.
• L-Broth L-Broth
• Miniprep plasmid DNA was prepared from the 5 ml culture using a Qiaprep Turbo 9600 robotic system (Qiagen) or Wizard Plus SV Minipreps kit (Promega cat. no. 1460) according to the manufacturer's instructions. Plasmid DNA was eluted in 100 ⁇ l of sterile water. The DNA concentration was measured using an Eppendorf BO photometer or Spectramax 190 Photometer (Molecular Devices). Plasmid DNA (100-200 ng) was subjected to DNA sequencing with the T7 primer and T3 primer using the BigDye Terminator system (Applied Biosystems cat. no. 4390246) according to the manufacturer's instructions. The primer sequences are shown in Table 1. Sequencing reactions were purified using Dye-Ex columns (Qiagen) or Montage SEQ 96 cleanup plates (Millipore cat. no. LSKS09624) then analyzed on an Applied Biosystems 3700 sequencer.
• Plasmid 14352 was used as a PCR template to generate pEAK12d ( Figure 11) and pDEST12.2 ( Figure 12) expression clones containing the INSP123 ORF sequence with a 3' sequence encoding a 6HJS tag using the GatewayTM cloning methodology (Invitrogen).
• the first stage of the Gateway cloning process involves a two step PCR reaction which generates the ORF of INSP123 flanked at the 5' end by an attBl recombination site and Kozak sequence, and flanked at the 3' end by a sequence encoding an in- frame 6 histidine (6HIS) tag, a stop codon and the attB2 recombination site (Gateway compatible cDNA).
• 6HIS in- frame 6 histidine
• the first PCR reaction (in a final volume of 50 ⁇ l) contains: 1 ⁇ l (40 ng) of plasmid 14352, 1.5 ⁇ l dNTPs (10 mM), 10 ⁇ l of 10X Pfx polymerase buffer, 1 ⁇ l MgS04 (50 mM), 0.5 ⁇ l each of gene specific primer (100 ⁇ M) (INSP123-EX1 and INSP123-EX2), and 0.5 ⁇ l Platinum Pfx DNA polymerase (Invitrogen).
• the PCR reaction was performed using an initial denaturing step of 95 °C for 2 min, followed by 12 cycles of 94 °C for 15 s; 55 °C for 30 s and 68 °C for 2 min; and a holding cycle of 4 °C.
• the amplification products were visualized on 0.8 % agarose gel in 1 X TAE buffer (Invitrogen) and a product migrating at the predicted molecular mass (447 bp) was purified from the gel using the Wizard PCR Preps DNA Purification System (Promega) and recovered in 50 ⁇ l sterile water according to the manufacturer's instructions.
• the second PCR reaction (in a final volume of 50 ⁇ l) contained 10 ⁇ l purified PCR 1 product, 1.5 ⁇ l dNTPs (10 mM), 5 ⁇ l of 10X Pfx polymerase buffer, 1 ⁇ l MgS04 (50 mM), 0.5 ⁇ l of each Gateway conversion primer (100 ⁇ M) (GCP forward and GCP reverse) and 0.5 ⁇ l of Platinum Pfx DNA polymerase.
• the conditions for the 2nd PCR reaction were: 95 °C for 1 min; 4 cycles of 94 °C, 15 sec; 50 °C, 30 sec and 68 °C for 2 min; 25 cycles of 94 °C, 15 sec; 55 °C , 30 sec and 68 °C, 2 min; followed by a holding cycle of 4 °C.
• PCR products were gel purified using the Wizard PCR prep DNA purification system (Promega) according to the manufacturer's instructions.
• Gateway compatible INSP123 ORF Subcloning of Gateway compatible INSP123 ORF into Gateway entry vector pDONR221 and expression vectors pEAK12d and pDEST12.2
• the second stage of the Gateway cloning process involves subcloning of the Gateway modified PCR product into the Gateway entry vector pDONR221 (Invitrogen, Figure 10) as follows: 5 ⁇ l of purified product from PCR2 were incubated with 1.5 ⁇ l pDONR221 vector (0.1 ⁇ g ul), 2 ⁇ l BP buffer and 1.5 ⁇ l of BP clonase enzyme mix (Invitrogen) in a final volume of 10 ⁇ l at RT for 1 h. The reaction was stopped by addition of proteinase K 1 ⁇ l (2 ⁇ g/ ⁇ l) and incubated at 37 °C for a further 10 min. An aliquot of this reaction (1 ⁇ l) was used to transform E.
• coli DH10B cells by electroporation as follows: a 25 ⁇ l aliquot of DH10B electrocompetent cells (Invitrogen) was thawed on ice and 1 ⁇ l of the BP reaction mix was added. The mixture was transferred to a chilled 0.1 cm electroporation cuvette and the cells electroporated using a BioRad Gene-PulserTM according to the manufacturer's recommended protocol. SOC media (0.5 ml) which had been pre- warmed to room temperature was added immediately after electroporation. The mixture was transferred to a 15 ml snap-cap tube and incubated, with shaking (220 ⁇ m), for 1 h at 37 °C. Aliquots of the transformation mixture (10 ⁇ l and 50 ⁇ l) were then plated on L-broth (LB) plates containing kanamycin (40 ⁇ g/ml) and incubated overnight at 37 °C.
• LB L-broth
• Plasmid mini-prep DNA was prepared from 5 ml cultures from 6 of the resultant colonies using a Qiaprep Turbo 9600 robotic system (Qiagen). Plasmid DNA (150-200 ng) was subjected to DNA sequencing with 21M13 and M13Rev primers using the BigDyeTerminator system (Applied Biosystems cat. no. 4390246) according to the manufacturer's instructions. The primer sequences are shown in Table 1. Sequencing reactions were purified using Dye-Ex columns (Qiagen) or Montage SEQ 96 cleanup plates (Millipore cat. no. LSKS09624) then analyzed on an Applied Biosystems 3700 sequencer.
• Plasmid eluate (2 ⁇ l or approx. 150 ng) from one of the clones which contained the correct sequence (pENTRJNSP123-6HIS, plasmid ID 14595, Figure 13) was then used in a recombination reaction containing 1.5 ⁇ l of either pEAK12d vector or pDEST12.2 vector ( Figures 11 & 12) (0.1 ⁇ g / ⁇ l), 2 ⁇ l LR buffer and 1.5 ⁇ l of LR clonase (Invitrogen) in a final volume of 10 ⁇ l.
• the mixture was incubated at RT for 1 h, stopped by addition of proteinase K (2 ⁇ g) and incubated at 37 °C for a further 10 min.
• Plasmid mini-prep DNA was prepared from 5 ml cultures from 6 of the resultant colonies subcloned in each vector using a Qiaprep Turbo 9600 robotic system (Qiagen). Plasmid DNA (200- 500 ng) in the pEAK12d vector was subjected to DNA sequencing with pEAK12F and pEAK12R primers as described above. Plasmid DNA (200-500 ng) in the pDEST12.2 vector was subjected to DNA sequencing with 21 Ml 3 and M13Rev primers as described above. Primer sequences are shown in Table 1.
• CsCl gradient purified maxi-prep DNA was prepared from a 500 ml culture of one of each of the sequence verified clones (pEAK12d_INSP123-6HIS, plasmid JD number 14602, Figure 8, and pDEST12.2_INSP123-6HIS, plasmid ED 14606, Figure 9) using the method described by Sambrook J. et al., 1989 (in Molecular Cloning, a Laboratory Manual, 2 nd edition, Cold Spring Harbor Laboratory Press), Plasmid DNA was resuspended at a concentration of 1 ⁇ g/ ⁇ l in sterile water (or 10 mM Tris-HCI pH 8.5) and stored at -20°C.
• INSP124 is a prediction for a full length SECFAM3 family novel secreted protein of 222 amino acids (666 bp) encoded in three coding exons ( Figures 16 & 17).
• Exon 1 was amplified from plasmid ID 14352 (containing INSP123, a splice variant of INSP124) by PCR.
• Exons 2 and 3 were amplified from genomic DNA by PCR ( Figure 17). - The gel-purified exons were mixed and a new PCR reaction was performed to amplify the re-assembled DNA.
• PCR primers were designed to amplify exons 1, 2 and 3 of INSP124 (Table 2).
• the reverse primer for exon 1 (INSP124-elR) has an overlap of 18 bp with exon 2 of INSP124 at its 5' end.
• the forward primer for exon 2 (INSP124 -e2F) has an 19 bp overlap with exon 1 of INSP124 at its 5' end.
• the reverse primer for exon 2 (INSP124-e2R) has an overlap of 19 bp with exon 3 of INSP124 at its 5' end.
• the forward primer for exon 3 (INSP124 -e3F) has an 18 bp overlap with exon 2 of INSP124 at its 5' end.
• the PCR reaction was performed in a final volume of 50 ⁇ l and contained 100 ng of plasmid ID 14352 DNA, IX AmpliTaqTM buffer, 200 ⁇ M dNTPs, 50 pmoles of INSP124-elF, 50 pmoles of INSP124-elR , and 2.5 units of AmpliTaqTM (Perkin Elmer) using an MJ Research DNA Engine, programmed as follows: 94 °C, 2 min; 30 cycles of 94 °C, 30 sec, 63 °C, 30 sec, and 72 °C, 1 min; followed by 1 cycle at 72 °C for 7 min and a holding cycle at 4 °C.
• the PCR reaction was performed in a final volume of 50 ⁇ l and contained 1 ⁇ l of genomic DNA (0.1 ⁇ g/ ⁇ l (Novagen Inc.), IX AmpliTaqTM buffer, 200 ⁇ M dNTPs, 50 pmoles of INSP124-e2F, 50 pmoles of INSP124-e2R , and 2.5 units of AmpliTaqTM (Perkin Elmer).
• the PCR reaction was performed in a final volume of 50 ⁇ l and contained 1 ⁇ l of genomic DNA (0.1 ⁇ g/ ⁇ l (Novagen Inc.), IX AmpliTaqTM buffer, 200 ⁇ M dNTPs, 50 pmoles of INSP124-e3F, 50 pmoles of INSP124-e3R , and 2.5 units of AmpliTaqTM (Perkin Elmer).
• PCR cycling to generate exon 2 and exon 3 used an MJ Research DNA Engine, programmed as follows: 94 °C, 2 min; 30 cycles of 94 °C, 30 sec, 65 °C, 30 sec, and 72 °C, 40 sec; followed by 1 cycle at 72 °C for 5 min and a holding cycle at 4 °C.
• Reaction products were analysed on a 1.8 % agarose gel (IX TAE) and PCR products of the correct size (439 bp, 168 bp, 171 bp for exons 1, 2 and 3, respectively) were gel-purified using the Wizard PCR Preps DNA Purification System (Promega) and eluted in 50 ⁇ l of water. Ten ⁇ l of each purified PCR product was visualised on a 1.8% agarose gel to estimate the concentration.
• Exons 1, 2 and 3 were assembled in a 50 ⁇ l PCR reaction containing 3 ⁇ l of gel purified exon 1, 5 ⁇ l of gel purified exon 2, 5 ⁇ l of gel purified exon 3, 1.5 ⁇ l of 10 mM dNTPs, 1 ⁇ l of MgS0 j 1.5 ⁇ l of INSP124-elF (10 ⁇ M), 1.5 ⁇ l of JNSP124-e3R (10 ⁇ M), 5 ⁇ l of 10X Platinum PfxTM buffer, and 0.5 ⁇ l of Platinum PfxTM DNA polymerase (5 U/ ⁇ l) (Invitrogen).
• reaction conditions were: 94 °C, 4 min; 10 cycles of 94 °C for 30 s, 48 °C for 30 s and 68 °C for 1 min; 25 cycles of 94 °C for 30 s, 52 °C for 30 s and 68 °C for 1 min; an additional elongation cycle of 68 °C for 10 min; and a holding cycle of 4 °C.
• Reaction products were analysed on a 0.8 % agarose gel (IX TAE). PCR products of the correct size (704 bp) were gel-purified using the Wizard PCR Preps DNA Purification System (Promega), eluted in 50 ⁇ l of water and subcloned directly.
• the PCR product was subcloned into the topoisomerase I modified cloning vector (pCR-Bluntll- TOPO) purchased from the Invitrogen Co ⁇ oration using the conditions specified by the manufacturer. Briefly, 4 ⁇ l of gel purified PCR product was incubated for 15 min at room temperature with 1 ⁇ l of TOPO vector and 1 ⁇ l salt solution. The reaction mixture was then transformed into E. coli strain TOP 10 (Invitrogen) as follows: a ⁇ l aliquot of One Shot TOP 10 cells was thawed on ice and 2 ⁇ l of TOPO reaction was added. The mixture was incubated for 15 min on ice and then heat shocked by incubation at 42 °C for exactly 30 s.
• E. coli strain TOP 10 Invitrogen
• Colonies were inoculated into 50 ⁇ l sterile water using a sterile toothpick. A 10 ⁇ l aliquot of the inoculum was then subjected to PCR in a total reaction volume of 20 ⁇ l containing IX AmpliTaqTM buffer, 200 ⁇ M dNTPs, 20 pmoles T7 primer, 20 pmoles of SP6 primer, 1 unit of AmpliTaqTM (Perkin Elmer) using an MJ Research DNA Engine. The cycling conditions were as follows: 94 °C, 2 min; 30 cycles of 94 °C, 30 sec, 48 °C, 30 sec and 72 °C for 1 min. Samples were maintained at 4 °C (holding cycle) before further analysis.
• PCR reaction products were analysed on 1 % agarose gels in 1 X TAE buffer. Colonies which gave the expected PCR product size (704 bp cDNA + 186 bp due to the multiple cloning site or MCS) were grown up overnight at 37 °C in 5 ml L-Broth (LB) containing kanamycin (40 ⁇ g /ml), with shaking at 220 ⁇ m.
• Miniprep plasmid DNA was prepared from 5 ml cultures using a Qiaprep Turbo 9600 robotic system (Qiagen) or Wizard Plus SV Minipreps kit (Promega cat. no. 1460) according to the manufacturer's instructions. Plasmid DNA was eluted in 100 ⁇ l of sterile water. The DNA concentration was measured using an Eppendorf BO photometer or a Spectramax 190 photometer (Molecular Devices). Plasmid DNA (200-500 ng) was subjected to DNA sequencing with the T7 and SP6 primers using the BigDyeTerminator system (Applied Biosystems cat. no. 4390246) according to the manufacturer's instructions. The primer sequences are shown in Table 2. Sequencing reactions were purified using Dye-Ex columns (Qiagen) or Montage SEQ 96 cleanup plates (Millipore cat. no. LSKS09624) then analyzed on an Applied Biosystems 3700 sequencer.
• Qiaprep Turbo 9600 robotic system Qiagen
• Example 11 Construction of mammalian cell expression vectors for INSP124 Plasmid 14649 was used as a PCR template to generate pEAK12d (figure 21) and pDEST12.2 (figure 22) expression clones containing the INSP124 ORF sequence with a 3' sequence encoding a 6HIS tag using the GatewayTM cloning methodology (Invitrogen).
• the first stage of the Gateway cloning process involves a two step PCR reaction which generates the ORF of INSP124 flanked at the 5' end by an attBl recombination site and Kozak sequence, and flanked at the 3' end by a sequence encoding an in-frame 6 histidine (6HIS) tag, a stop codon and the attB2 recombination site (Gateway compatible cDNA).
• 6HIS in-frame 6 histidine
• the first PCR reaction (in a final volume of 50 ⁇ l) contains: 1 ⁇ l (40 ng) of plasmid 14649, 1.5 ⁇ l dNTPs (10 mM), 10 ⁇ l of 10X Pfx polymerase buffer, 1 ⁇ l MgS04 (50 mM), 0.5 ⁇ l each of gene specific primer (100 ⁇ M) (INSP124-EX1 and JNSP124-EX2), and 0.5 ⁇ l Platinum Pfx DNA polymerase (Invitrogen).
• the PCR reaction was performed using an initial denaturing step of 95 °C for 2 min, followed by 12 cycles of 94 °C for 15 s; 55 °C for 30 s and 68 °C for 2 min; and a holding cycle of 4 °C.
• the amplification products were visualized on 0.8 % agarose gel in 1 X TAE buffer (Invitrogen) and a product migrating at the predicted molecular mass (699 bp) was purified from the gel using the Wizard PCR Preps DNA Purification System (Promega) and recovered in 50 ⁇ l sterile water according to the manufacturer's instructions.
• the second PCR reaction (in a final volume of 50 ⁇ l) contained 10 ⁇ l purified PCR 1 product, 1.5 ⁇ l dNTPs (10 mM), 5 ⁇ l of 10X Pfx polymerase buffer, 1 ⁇ l MgS04 (50 mM), 0.5 ⁇ l of each Gateway conversion primer (100 ⁇ M) (GCP forward and GCP reverse) and 0.5 ⁇ l of Platinum Pfx DNA polymerase.
• the conditions for the 2nd PCR reaction were: 95 °C for 1 min; 4 cycles of 94 °C, 15 sec; 50 °C, 30 sec and 68 °C for 2 min; 25 cycles of 94 °C, 15 sec; 55 °C , 30 sec and 68 °C, 2 min; followed by a holding cycle of 4 °C.
• PCR products were gel purified using the Wizard PCR prep DNA purification system (Promega) according to the manufacturer's instructions.
• Gateway compatible INSP124 ORF into Gateway entry vector pDONR221 and expression vectors pEAK12d and pDEST12.2
• the second stage of the Gateway cloning process involves subcloning of the Gateway modified PCR product into the Gateway entry vector pDONR221 (Invitrogen, figure 20) as follows: 5 ⁇ l of purified product from PCR2 were incubated with 1.5 ⁇ l pDONR221 vector (0.1 ⁇ g/ ⁇ l), 2 ⁇ l BP buffer and 1.5 ⁇ l of BP clonase enzyme mix (Invitrogen) in a final volume of 10 ⁇ l at RT for 1 h.
• the reaction was stopped by addition of proteinase K (1 ⁇ l at 2 ⁇ g/ ⁇ l) and incubated at 37 °C for a further 10 min.
• An aliquot of the reaction (1 ⁇ l) was used to transform E. coli DH10B cells by electroporation as follows: a 25 ⁇ l aliquot of DH10B electrocompetent cells (Invitrogen) was thawed on ice and 1 ⁇ l of the BP reaction mix was added. The mixture was transferred to a chilled 0.1 cm electroporation cuvette and the cells electroporated using a BioRad Gene-PulserTM according to the manufacturer's recommended protocol.
• SOC media (0.5 ml) which had been pre- warmed to room temperature was added immediately after electroporation. The mixture was transferred to a 15 ml snap-cap tube and incubated, with shaking (220 ⁇ m) for 1 h at 37 °C. Aliquots of the transformation mixture (10 ⁇ l and 50 ⁇ l) were then plated on L-broth (LB) plates containing kanamycin (40 ⁇ g/ml) and incubated overnight at 37 °C.
• LB L-broth
• Plasmid mini-prep DNA was prepared from 5 ml cultures from 6 of the resultant colonies using a Qiaprep Turbo 9600 robotic system (Qiagen). Plasmid DNA (150-200 ng) was subjected to DNA sequencing with 21M13 and M13Rev primers using the BigDyeTerminator system (Applied Biosystems cat. no. 4390246) according to the manufacturer's instructions. The primer sequences are shown in Table 1. Sequencing reactions were purified using Dye-Ex columns (Qiagen) or Montage SEQ 96 cleanup plates (Millipore cat. no. LSKS09624) then analyzed on an Applied Biosystems 3700 sequencer.
• Plasmid eluate (2 ⁇ l or approx. 150 ng) from one of the clones which contained the correct sequence (pENTR_INSP124-6HIS, plasmid JD 14690, figure 23) was then used in a recombination reaction containing 1.5 ⁇ l of either pEAKl 2d vector or pDEST12.2 vector (figures 21 & 22) (0.1 ⁇ g / ⁇ l), 2 ⁇ l LR buffer and 1.5 ⁇ l of LR clonase (Invitrogen) in a final volume of 10 ⁇ l.
• SOC media (0.5 ml) which had been pre- warmed to room temperature was added immediately after electroporation. The mixture was transferred to a 15 ml snap-cap tube and incubated, with shaking (220 ⁇ m) for 1 h at 37 °C. Aliquots of the transformation mixture (10 ⁇ l and 50 ⁇ l) were then plated on L-broth (LB) plates containing ampicillin (100 ⁇ g/ml) and incubated overnight at 37 °C.
• LB L-broth
• Plasmid mini-prep DNA was prepared from 5 ml cultures from 6 of the resultant colonies subcloned in each vector using a Qiaprep Turbo 9600 robotic system (Qiagen). Plasmid DNA (200- 500 ng) in the pEAK12d vector was subjected to DNA sequencing with pEAK12F and pEAK12R primers as described above. Plasmid DNA (200-500 ng) in the pDEST12.2 vector was subjected to DNA sequencing with 21M13 and M13Rev primers as described above. Primer sequences are shown in Table 2.
• CsCl gradient purified maxi-prep DNA was prepared from a 500 ml culture from one of each of the sequence verified clones (pEAK12d_INSP124-6HIS, plasmid JD number 14697, figure 24, and pDEST12.2_INSP124-6HIS, plasmid ED 14698, figure 25) using the method described by Sambrook J. et al., 1989 (in Molecular Cloning, a Laboratory Manual, 2 nd edition, Cold Spring Harbor Laboratory Press). Plasmid DNA was resuspended at a concentration of 1 ⁇ g/ ⁇ l in sterile water (or 10 mM Tris-HCI pH 8.5) and stored at -20 °C.
• INSP125 is a prediction for a full length SECFAM3 family novel secreted protein of 175 amino acids (525 bp) ( Figure 26).
• the predicted JNSP125 coding sequence was identical to the predicted INSP124 coding sequence except that it contains a 47 amino acid (141 bp) deletion.
• the ESfSP124 prediction had previously been cloned (pCR-BluntII-TOPO-INSP124, plasmid TD 14649).
• Exons 2-4 were amplified as a single product from plasmid ID 14649 by PCR.
• PCR primers were designed to amplify exon 1 and exons 2-4 of INSP125 (Table 3).
• the reverse primer for exon 1 (INSP125-elR) has an overlap of 19 bp with exon 2 of INSP125 at its 5' end.
• the forward primer for exon 2 (INSP125 -e2F) has an 18 bp overlap with exon 1 of INSP125 at its 5' end.
• the primers INSP124-elF and INSP124-e3R were used as the forward and reverse primers to amplify the exon fragments, and ultimately the whole BSTSP125 coding sequence.
• the PCR reaction was performed in a final volume of 50 ⁇ l containing 100 ng of plasmid ED 14649 DNA, 1.5 ⁇ l of 10 mM dNTPs, 1 ⁇ l of MgS0 4, 1.5 ⁇ l of INSP124-elF (10 ⁇ M), 1.5 ⁇ l of ENSP125-elR (10 ⁇ M), 5 ⁇ l of 10X Platinum PfxTM buffer, and 0.5 ⁇ l of Platinum PfxTM DNA polymerase (5 U/ ⁇ l) (Invitrogen).
• the reaction conditions were: 94 °C, 2 min; 30 cycles of 94 °C for 15 s, 61 °C for 30 s and 68 °C for 1 min ; an additional elongation cycle of 68 °C for 7 min; and a holding cycle of 4 °C.
• the expected product size was 150 bp.
• exons 2-4 of EMSP125 the PCR reaction was performed exactly as for exon 1 above, except that the amplification primers used were JNSP125-e2F and INSP124-e3R.
• the expected product size was 450 bp.
• Reaction products were loaded onto a 1.5 % agarose gel (IX TAE) and PCR products of the correct size (150 bp and 450 bp) were gel-purified using the Qiagen MinElute DNA purification system (Qiagen) according to the manufacturer's instructions, and eluted in 10 ⁇ l of EB buffer (lOmM
• Exon 1 and the exon 2-4 product were assembled in a 50 ⁇ l PCR reaction containing 1 ⁇ l of gel purified exon 1, 1 ⁇ l of gel purified exon 2-4 product, 1 ⁇ l of 10 mM dNTPs, 2 ⁇ l of MgS0 4 ⁇ 1 ⁇ l of ENSP124-elF (10 ⁇ M), 1 ⁇ l of fNSP124-e3R (10 ⁇ M), 5 ⁇ l of 10X Platinum Taq HiFi buffer, and 0.5 ⁇ l of Platinum Taq HiFi DNA polymerase (5 U/ ⁇ l) (Invitrogen).
• reaction conditions were: 94 °C, 2 min; 10 cycles of 94 °C for 30 s, 48 °C for 30 s and 68 °C for 1 min; 25 cycles of 94 °C for 30 s, 52 °C for 30 s and 68 °C for 1 min; an additional elongation cycle of 68 °C for 7 min; and a holding cycle of 4 °C.
• Reaction products were analysed on a 1 % agarose gel (IX TAE). PCR products of the correct size (563 bp) were gel-purified using the Wizard PCR Preps DNA Purification System (Promega), eluted in 50 ⁇ l of water and subcloned directly.
• the PCR product was subcloned into the topoisomerase I modified cloning vector (pCR4-TOPO) purchased from the Invitrogen Co ⁇ oration using the conditions specified by the manufacturer. Briefly, 4 ⁇ l of gel purified PCR product was incubated for 15 min at room temperature with 1 ⁇ l of TOPO vector and 1 ⁇ l salt solution. The reaction mixture was then transformed into E. coli strain TOP10 (Invitrogen) as follows: a 50 ⁇ l aliquot of One Shot TOP10 cells was thawed on ice and 2 ⁇ l of TOPO reaction was added. The mixture was incubated for 15 min on ice and then heat shocked by incubation at 42 °C for exactly 30 s.
• pCR4-TOPO topoisomerase I modified cloning vector
• Samples were returned to ice and 250 ⁇ l of warm (room temperature) SOC media was added. Samples were incubated with shaking (220 ⁇ m) for 1 h at 37 °C. The transformation mixture was then plated on L-broth (LB) plates containing amplicillin (100 ⁇ g/ml) and incubated overnight at 37 °C.
• LB L-broth
• Colony PCR Colonies were inoculated into 50 ⁇ l sterile water using a sterile toothpick. A 10 ⁇ l aliquot of the inoculum was then subjected to PCR in a total reaction volume of 20 ⁇ l containing IX AmpliTaqTM buffer, 200 ⁇ M dNTPs, 20 pmoles of T7 primer, 20 pmoles of T3 primer, 1 unit of AmpliTaqTM (Perkin Elmer) using an MJ Research DNA Engine. The cycling conditions were as follows: 94 °C, 2 min; 30 cycles of 94 °C, 30 sec, 48 °C, 30 sec and 72 °C for 1 min. Samples were maintained at 4 °C (holding cycle) before further analysis.
• PCR reaction products were analyzed on a 1 % agarose gel in 1 X TAE buffer. Colonies which gave the expected PCR product size (563 bp cDNA + 105 bp due to the multiple cloning site or MCS) were grown up overnight at 37 °C in 5 ml L-Broth (LB) containing ampicillin (100 ⁇ g /ml), with shaking at 220 ⁇ m.
• L-Broth L-Broth
• Miniprep plasmid DNA was prepared from the 5 ml culture using a Qiaprep Turbo 9600 robotic system (Qiagen) or Wizard Plus SV Minipreps kit (Promega cat. no. 1460) according to the manufacturer's instructions. Plasmid DNA was eluted in 100 ⁇ l of sterile water. The DNA concentration was measured using an Eppendorf BO photometer or a Spectramax 190 photometer (Molecular Devices). Plasmid DNA (100-200 ng) was subjected to DNA sequencing with the T7 and T3 primers using the BigDyeTerminator system (Applied Biosystems cat. no. 4390246) according to the manufacturer's instructions. The primer sequences are shown in Table 1. Sequencing reactions were purified using Dye-Ex columns (Qiagen) or Montage SEQ 96 cleanup plates (Millipore cat. no. LSKS09624) then analyzed on an Applied Biosystems 3700 sequencer.
• Qiaprep Turbo 9600 robotic system Qia
• Sequence analysis identified a clone containing 100% match to the predicted INSP125 sequence.
• the sequence of the cloned cDNA fragment is shown in Figure 3.
• the plasmid map of the cloned PCR product (pCR4-TOPO-INSP125, plasmid ED. 14681) is shown in Figure 29.
• Example 13 Construction of mammalian cell expression vectors for ENSP125 Plasmid 14681 was used as a PCR template to generate pEAK12d ( Figure 31) and pDEST12.2 ( Figure 32) expression clones containing the INSP125 ORF sequence with a 3' sequence encoding a 6HIS tag using the GatewayTM cloning methodology (Invitrogen).
• the first stage of the Gateway cloning process involves a two step PCR reaction which generates the ORF of ENSP125 flanked at the 5' end by an attBl recombination site and Kozak sequence, and flanked at the 3' end by a sequence encoding an in frame 6 histidine (6HIS) tag, a stop codon and the attB2 recombination site (Gateway compatible cDNA).
• 6HIS in frame 6 histidine
• the first PCR reaction (in a final volume of 50 ⁇ l) contains: 1 ⁇ l (40 ng) of plasmid 14681, 1.5 ⁇ l dNTPs (10 mM), 10 ⁇ l of 10X Pfx polymerase buffer, 1 ⁇ l MgS04 (50 mM), 0.5 ⁇ l each of gene specific primer (100 ⁇ M) (INSP125-EX1 and INSP125-EX2), and 0.5 ⁇ l Platinum Pfx DNA polymerase (Invitrogen).
• the PCR reaction was performed using an initial denaturing step of 95 °C for 2 min, followed by 12 cycles of 94 °C for 15 s; 55 °C for 30 s and 68 °C for 2 min; and a holding cycle of 4 °C.
• the amplification products were visualized on 0.8 % agarose gel in 1 X TAE buffer (Invitrogen) and a product migrating at the predicted molecular mass (593 bp) was purified from the gel using the Wizard PCR Preps DNA Purification System (Promega) and recovered in 50 ⁇ l sterile water according to the manufacturer's instructions.
• the second PCR reaction (in a final volume of 50 ⁇ l) contained 10 ⁇ l purified PCR 1 product, 1.5 ⁇ l dNTPs (10 mM), 5 ⁇ l of 10X Pfx polymerase buffer, 1 ⁇ l MgS04 (50 mM), 0.5 ⁇ l of each Gateway conversion primer (100 ⁇ M) (GCP forward and GCP reverse) and 0.5 ⁇ l of Platinum Pfx DNA polymerase.
• the conditions for the 2nd PCR reaction were: 95 °C for 1 min; 4 cycles of 94 °C, 15 sec; 50 °C, 30 sec and 68 °C for 2 min; 25 cycles of 94 °C, 15 sec; 55 °C , 30 sec and 68 °C, 2 min; followed by a holding cycle of 4 °C.
• PCR products were gel purified using the Wizard PCR prep DNA purification system (Promega) according to the manufacturer's instructions.
• Gateway compatible INSP125 ORF into Gateway entry vector ⁇ DONR221 and expression vectors pEAK12d and pDEST12.2
• the second stage of the Gateway cloning process involves subcloning of the Gateway modified PCR product into the Gateway entry vector pDONR221 (Invitrogen, Figure 30) as follows: 5 ⁇ l of purified product from PCR2 were incubated with 1.5 ⁇ l pDONR221 vector (0.1 ⁇ g/ ⁇ l), 2 ⁇ l BP buffer and 1.5 ⁇ l of BP clonase enzyme mix (Invitrogen) in a final volume of 10 ⁇ l at RT for 1 h.
• the reaction was stopped by addition of proteinase K (1 ⁇ l at 2 ⁇ g/ ⁇ l) and incubated at 37 °C for a further 10 min.
• An aliquot of this reaction (1 ⁇ l) was used to transform E. coli DH10B cells by electroporation as follows: a 25 ⁇ l aliquot of DH10B electrocompetent cells (Invitrogen) was thawed on ice and 1 ⁇ l of the BP reaction mix was added. The mixture was transferred to a chilled 0.1 cm electroporation cuvette and the cells electroporated using a BioRad Gene-PulserTM according to the manufacturer's recommended protocol.
• SOC media (0.5 ml) which had been pre- warmed to room temperature was added immediately after electroporation. The mixture was transferred to a 15 ml snap-cap tube and incubated, with shaking (220 ⁇ m) for 1 h at 37 °C. Aliquots of the transformation mixture (10 ⁇ l and 50 ⁇ l) were then plated on L-broth (LB) plates containing kanamycin (40 ⁇ g/ml) and incubated overnight at 37 °C.
• LB L-broth
• Plasmid mini-prep DNA was prepared from 5 ml cultures from 6 of the resultant colonies using a Qiaprep Turbo 9600 robotic system (Qiagen). Plasmid DNA (150-200 ng) was subjected to DNA sequencing with 21M13 and M13Rev primers using the BigDyeTerminator system (Applied Biosystems cat. no. 4390246) according to the manufacturer's instructions. The primer sequences are shown in Table 3. Sequencing reactions were purified using Dye-Ex columns (Qiagen) or Montage SEQ 96 cleanup plates (Millipore cat. no. LSKS09624) then analyzed on an Applied Biosystems 3700 sequencer.
• Plasmid eluate (2 ⁇ l or approx. 150 ng) from one of the clones which contained the correct sequence (pENTR_INSP125-6HIS, plasmid ED 14876, Figure 33) was then used in a recombination reaction containing 1.5 ⁇ l of either pEAK12d vector or pDEST12.2 vector ( Figures 31 & 32) (0.1 ⁇ g / ⁇ l), 2 ⁇ l LR buffer and 1.5 ⁇ l of LR clonase (Invitrogen) in a final volume of 10 ⁇ l.
• the mixture was incubated at RT for 1 h, stopped by addition of proteinase K (2 ⁇ g) and incubated at 37 °C for a further 10 min.
• the mixture was transferred to a 15 ml snap-cap tube and incubated, with shaking (220 ⁇ m) for 1 h at 37 °C. Aliquots of the transformation mixture (10 ⁇ l and 50 ⁇ l) were then plated on L-broth (LB) plates containing ampicillin (100 ⁇ g/ml) and incubated overnight at 37 °C.
• LB L-broth
• Plasmid mini-prep DNA was prepared from 5 ml cultures from 6 of the resultant colonies subcloned in each vector using a Qiaprep Turbo 9600 robotic system (Qiagen). Plasmid DNA (200- 500 ng) in the pEAK12d vector was subjected to DNA sequencing with pEAK12F and pEAK12R primers as described above. Plasmid DNA (200-500 ng) in the pDEST12.2 vector was subjected to DNA sequencing with 21M13 and M13Rev primers as described above. Primer sequences are shown in Table 3.
• CsCl gradient purified maxi-prep DNA was prepared from a 500 ml culture of one of each of the sequence verified clones (pEAK12d_INSP125-6HIS, plasmid JD number 14882, Figure 34, and pDEST12.2_INSP125-6HIS, plasmid ED 14886, Figure 35) using the method described by Sambrook J. et al., 1989 (in Molecular Cloning, a Laboratory Manual, 2 nd edition, Cold Spring Harbor Laboratory Press), Plasmid DNA was resuspended at a concentration of 1 ⁇ g/ ⁇ l in sterile water (or 10 mM Tris-HCI pH 8.5) and stored at -20 °C.
• RNA from each tissue may be used to generate cDNA using Multiscript reverse transcriptase (ABI) and random hexamer primers.
• ABSI Multiscript reverse transcriptase
• a control reaction is set up in which all the constituents are added except the reverse transcriptase (-ve RT control).
• PCR reactions are set up for each tissue on the reverse transcribed RNA samples and the minus RT controls.
• INSP123, INSP124 and INSP125-specific primers may readily be designed on the basis of the sequence information provided herein.
• the presence of a product of the correct molecular weight in the reverse transcribed sample together with the absence of a product in the minus RT control may be taken as evidence for the presence of a transcript in that tissue.
• Any suitable cDNA libraries may be used to screen for the EMSP123, ENTSP124 and JNSP125 transcripts, not only those generated as described above.
• tissue distribution pattern of the INSP123, INSP124 and INSP125 polypeptides will provide further useful information in relation to the function of those polypeptides.
• further experiments may now be performed using the pCR4-TOPO-INSP123 (figure 9), pDONR (figure 10), pEAK12d (figure 11), pDEST12.2 (figure 12), pENTR-INSP123-6HIS (figure 13), pEAK12d-INSP123-6HIS (figure 14), pDEST12.2-INSP123-6HIS (figure 15), pCR4- BluntII-TOPO-INSP124 (figure 19), pDONR 221 (figure 20),.
• pEAK12d (figure 21), pDEST12.2 (figure 22), pENTR_INSP124-6HIS (figure 23), pEAK12d_INSP124-6HIS (figure 24), pDEST12.2_ INSP124-6HIS (figure 25), pCR4-TOPO-INSP125 (figure 29), pDONR 221 (figure 30), pEAK12d (figure 31), pDEST12.2 (figure 32), pENTR_INSP125-6HIS (figure 33), pEAK12d_INSP125-6HIS (figure 34) and pDEST12.2_ L SP125-6HIS (figure 35) expression vectors.
• Transfection of mammalian cell lines with these vectors may enable the high level expression of the INSP123, INSP124 and INSP125 proteins and thus enable the continued investigation of the functional characteristics of the EMSP123, INSP124 and JNSP125 polypeptides.
• the following material and methods are an example of those suitable in such experiments:
• Human Embryonic Kidney 293 cells expressing the Epstein-Barr virus Nuclear Antigen (HEK293- EBNA, Invitrogen) are maintained in suspension in Ex-cell VPRO serum-free medium (seed stock, maintenance medium, JRH).
• Ex-cell VPRO serum-free medium seed stock, maintenance medium, JRH.
• cells are seeded in 2x T225 flasks (50ml per flask in DMEM / F12 (1 :1) containing 2% FBS seeding medium (JRH) at a density of 2x10 5 cells/ml).
• plasmid DNA is co-transfected with GFP (fluorescent reporter gene) DNA.
• GFP fluorescent reporter gene
• the transfection mix is then added to the 2xT225 flasks and incubated at 37°C (5%C0 2 ) for 6 days. Confirmation of positive transfection may be carried out by qualitative fluorescence examination at day 1 and day 6 (Axiovert 10 Zeiss).
• Scale-up batches may be produced by following the protocol called "PEI transfection of suspension cells", referenced BP/PEJ7HH/02/04, with PolyEthylenelmine from Polysciences as transfection agent.
• the culture medium sample containing the recombinant protein with a C-terminal 6His tag is diluted with cold buffer A (50mM NaH 2 P0 4 ; 600mM NaCl; 8.7 % (w/v) glycerol, pH 7.5).
• the sample is filtered then through a sterile filter (Millipore) and kept at 4°C in a sterile square media bottle (Nalgene).
• the purification is performed at 4°C on the VISION workstation (Applied Biosystems) connected to an automatic sample loader (Labomatic).
• the purification procedure is composed of two sequential steps, metal affinity chromatography on a Poros 20 MC (Applied Biosystems) column charged with Ni ions (4.6 x 50 mm, 0.83ml), followed by gel filtration on a Sephadex G-25 medium (Amersham Pharmacia) column (1 ,0 x 10cm).
• the metal affinity column is regenerated with 30 column volumes of EDTA solution (lOOmM EDTA; 1M NaCl; pH 8.0), recharged with Ni ions through washing with 15 column volumes of a lOOmM NiS0 solution, washed with 10 column volumes of buffer A, followed by 7 column volumes of buffer B (50 mM NaH 2 P0 4 ; 600mM NaCl; 8.7 % (w/v) glycerol, 400mM; imidazole, pH 7.5), and finally equilibrated with 15 column volumes of buffer A containing 15mM imidazole.
• EDTA solution lOOmM EDTA; 1M NaCl; pH 8.0
• the sample is transferred, by the Labomatic sample loader, into a 200ml sample loop and subsequently charged onto the Ni metal affinity column at a flow rate of lOml/min.
• the column is washed with 12 column volumes of buffer A, followed by 28 column volumes of buffer A containing 20mM imidazole. During the 20mM imidazole wash loosely attached contaminating proteins are eluted from the column.
• the recombinant His-tagged protein is finally eluted with 10 column volumes of buffer B at a flow rate of 2ml/min, and the eluted protein is collected.
• the Sephadex G-25 gel-filtration column is regenerated with 2ml of buffer D (1.137M NaCl; 2.7mM KCl; 1.5mM KH 2 P0 4 ; 8mM Na 2 HP0 4 ; pH 7.2), and subsequently equilibrated with 4 column volumes of buffer C (137mM NaCl; 2.7mM KCl; 1.5mM KH 2 P0 4 ; 8mM Na 2 HP0 4 ; 20% (w/v) glycerol; pH 7.4).
• buffer D (1.137M NaCl; 2.7mM KCl; 1.5mM KH 2 P0 4 ; 8mM Na 2 HP0 4 ; pH 7.2
• buffer C 137mM NaCl; 2.7mM KCl; 1.5mM KH 2 P0 4 ; 8mM Na 2 HP0 4 ; 20% (w/v) glycerol; pH 7.4
• the peak fraction eluted from the Ni- column is automatically loaded onto the Sephadex G-25 column through the integrated sample loader on the VISION and the protein is eluted with buffer C at a flow rate of 2 ml/min.
• the fraction was filtered through a sterile centrifugation filter (Millipore), frozen and stored at — 80°C.
• An aliquot of the sample is analyzed on SDS-PAGE (4-12% NuPAGE gel; Novex) Western blot with anti-His antibodies.
• the NuPAGE gel may be stained in a 0.1 % Coomassie blue R250 staining solution (30% methanol, 10% acetic acid) at room temperature for lh and subsequently destained in 20% methanol, 7.5% acetic acid until the background is clear and the protein bands clearly visible. Following the electrophoresis the proteins are electrotransferred from the gel to a nitrocellulose membrane.
• the membrane is blocked with 5% milk powder in buffer E (137mM NaCl; 2.7mM KCl; 1.5mM KH 2 P0 4 ; 8mM Na 2 HP0 4 ; 0.1 % Tween 20, pH 7.4) for lh at room temperature, and subsequently incubated with a mixture of 2 rabbit polyclonal anti-His antibodies (G-18 and H-l 5, 0.2 ⁇ g/ml each; Santa Cruz) in 2.5% milk powder in buffer E overnight at 4°C.
• buffer E 137mM NaCl; 2.7mM KCl; 1.5mM KH 2 P0 4 ; 8mM Na 2 HP0 4 ; 0.1 % Tween 20, pH 7.
• the membrane After a further 1 hour incubation at room temperature, the membrane is washed with buffer E (3 x lOmin), and then incubated with a secondary HRP -conjugated anti-rabbit antibody (DAKO, HRP 0399) diluted 1/3000 in buffer E containing 2.5% milk powder for 2 hours at room temperature. After washing with buffer E (3 x 10 minutes), the membrane is developed with the ECL kit (Amersham Pharmacia) for 1 min. The membrane is subsequently exposed to a Hyperfilm (Amersham Pharmacia), the film developed and the western blot image visually analysed.
• DAKO secondary HRP -conjugated anti-rabbit antibody
• the protein concentration may be detennined using the BCA protein assay kit (Pierce) with bovine serum albumin as standard.
• overexpression or knock-down of the expression of the polypeptides in cell lines may be used to determine the effect on transcriptional activation of the host cell genome.
• Dimerisation partners, co-activators and co-repressors of the INSP123, INSP124 and ESTSP125 polypeptide may be identified by immunoprecipitation combined with Western blotting and immunoprecipitation combined with mass spectroscopy.
• Example 15 Assays for the detection of biological activity similar to that of secreted proteins containing a von Willebrand Factor type C.
• Oligodendrocytes are responsible for myelin formation in the CNS. In multiple sclerosis they are the first cells attacked and their loss leads to major behavioral impairment. In addition to curbing inflammation, enhancing the incomplete remyelination of lesions that occurs in MS has been proposed as a therapeutic strategy for MS. Like neurons, mature oligodendrocytes do not divide but the new oligodendrocytes can arise from progenitors. There are very few of these progenitor cells in adult brain and even in embryos the number of progenitor cells is inadequate for HTS.
• Oli-neu is a murine cell line obtained by an immortalization of an oligodendrocyte precursor by the t-neu oncogene. They are well studied and accepted as a representative cell line to study young oligodendrocyte biology.
• M03-13 results from the fusion of rabdo-myosarcoma cells with adult human oligodendrocytes. However these cells have a reduced ability to differentiate into oligodendrocytes and their proliferating rate is not sufficient to allow a proliferation assay. Nevertheless, they express certain features of oligodendrocytes and their mo ⁇ hology is well adapted to nuclear translocation studies.
• this cell line can be used in assays based on nuclear translocation of three transcription factors, respectively NF-kB, Stat-1 and Stat-2.
• the Jak/Stats transcription pathway is a complex pathway activated by many factors such as EFN ⁇ , ⁇ , ⁇ , cytokines (e.g. IL-2, JL-6; 1L-5) or hormones (e.g. GH, TPO, EPO).
• EFN ⁇ , ⁇ , ⁇ , cytokines e.g. IL-2, JL-6; 1L-5) or hormones (e.g. GH, TPO, EPO).
• the specificity of the response depends on the combination of activated Stats. For example, it is noticeable that EFN- ⁇ activates Statl, 2 and 3 nuclear translocations meanwhile EFN- ⁇ only activates Statl. In the same way, many cytokines and growth factors induced NF-kB translocation. In these assays the goal is to get a picture of activated pathways for a given protein.
• astrocytes The biology of astrocytes is very complex, but two general states are recognized. In one state called quiescent, astrocytes regulate the metabolic and excitatory level of neurons by pumping glutamate and providing energetic substratum to neurons and oligodendrocytes. In the activated state, astrocytes produce chemokines and cytokines as well as nitric oxide. The first state could be considered as normal healthy while the second state occurs during inflammation, stroke or neurodegenerative diseases. When this activated state persists it should be regarded as a pathological state.
• astrocyte activation Many factors and many pathways are known to modulate astrocyte activation.
• U373 cells a human cell line of astroglioma origin, can be used.
• NF-kB, c-Jun as well as Stats are signaling molecules known to play pivotal roles in astrocyte activation.
• a series of screens based on the nuclear translocation of NF-kB, c-Jun and Statl, 2 and 3 can be carried out.
• Prototypical activators of these pathways are EL- lb, EFN-beta or JFN-gamma. The goal is to identify proteins that could be used as therapeutics in the treatment of CNS diseases.
• Neurons are very complex and diverse cells but they have all in common two things. First they are post-mitotic cells, secondly they are innervating other cells. Their survival is linked to the presence of trophic factors often produced by the innervated target cells. In many neurodegenerative diseases the lost of target innervation leads to cell body atrophy and apoptotic cell death. Therefore identification of trophic factors supplementing target deficiency is very important in treatment of neurodegenerative diseases.
• NS1 cells a sub-clone of rat PC 12 cells.
• These cells have been used for years and a lot of neurobiology knowledge has been first acquired on these cells before being confirmed on primary neurons including the pathways involved in neuron survival and differentiation (MEK, PI3K, CREB).
• MEK, PI3K, CREB the pathways involved in neuron survival and differentiation
• N2A cells a mouse neuroblastoma
• Jun-kinase inhibitors prevent apoptosis induced by serum deprivation. Therefore assays on these two cell lines will help to find different types of "surviving promoting" proteins.
• the blood brain barrier (BBB) between brain and vessels is responsible of differences between cortical spinal fluid and serum compositions.
• the BBB results from a tight contact between endothelial cells and astrocytes. It maintains an immunotolerant status by preventing leukocytes penetration in brain, and allows the development of two parallels endocrine systems using the same intracellular signaling pathways.
• the BBB integrity is altered and leukocytes as well as serum proteins enter the brain inducing neuroinflammation.
• primary endothelial cells such as human embryonic umbilical endothelial cells (HUVEC) could mimic some aspect of BBB biology.
• BBB leakiness could be induced by proteins stimulating intracellular calcium release.
• a calcium mobilization assay with or without thrombin can be performed on HUVEC.
• SEQ ID 1 (INSP123 nucleotide sequence. Single exon.)
• SEQ ID 2 (INSP123 protein sequence. Single exon.)
• SEQ ID 4 (INSP123 mature protein sequence - signal peptide cleaved 23:24aa) 1 ISHEDYPADE GDQISSNDNL IFDDYRGKGC VDDSGFVYK GERFFPGHSN CPCVCALDGP 61 VCDQPECPKI HPKCTKVEHN GCCPECKEVK NFCEYHGKNY KILEEFKVCV TLHIY
• SEQ ID 7 (INSP124 nucleotide sequence, second exon) 1 CCCTCTCCAT GTGAATGGTG TCGCTGTGAG CCCAGCAATG AAGTTCACTG TGTTGTAGCA 61 GACTGCGCAG TTCCTGAGTG TGTCAACCCA GTCTATGAAC CAGAACAATG TTGTCCTGTC 121 TGCAAAAATG
• SEQ ID 8 (INSP124 protein sequence, second exon) 1 PSPCEWCRCE PSNEVHCWA DCAVPECVNP VYEPEQCCPV CKNG
• SEQ ID 12 (INSP124 full protein sequence) 1 MALHIHEACI LLLVIPGLVT SAAISHEDYP ADEGDQISSN DNLIFDDYRG KGCVDDSGFV
• SEQ ID 14 (INSP124 mature protein sequence first exon - signal peptide cleaved 23:24aa) 1 ISHEDYPADE GDQISSNDNL IFDDYRGKGC VDDSGFVYKL GERFFPGHSN CPCVCALDGP 61 VCDQPECPKI HPKCTKVEHN GCCPECKEVK NFCEYHGKNY KILEEFK
• SEQ ID 18 (INSP125 protein sequence, first exon)
• SEQ ID 20 (INSP125 protein sequence, second exon) 1 GPVCDQPECP KIHPKCTKVE HNGCCPECKE VKNFCEYHGK NYKILEEFK
• SEQ ID 22 (INSP125 protein sequence, third exon)
• SEQ ID 24 (INSP 125 protein sequence, fourth exon)
• SEQ ID 26 (INSP 125 full protein sequence) 1 MALHIHEACI LLLVIPGLVT SAAISHEDYP ADEDGPVCDQ PECPKIHPKC TKVEHNGCCP 61 ECKEVKNFCE YHGKNYKILE EFKPSPCEWC RCEPSNEVHC WADCAVPEC VNPVYEPEQC 121 CPVCKNGPNC FAGTTIIPAG IEVKVDECNI CHCHNGDWWK PAQCSKRECQ GKQTV
• SEQ ID 27 (INSP 125 mature protein CDS first exon - signal peptide cleaved 23:24aa) 1 ATCAGTCATG AAGACTATCC TGCTGATGAA G
• SEQ ID 28 (INSP 125 mature protein first exon - signal peptide cleaved 23:24aa)
• SEQ ID 39 (INSP 123 cloned polypeptide sequence) 1 MALHIHEACI LLLVIPGLVT SAAISHEDYP ADEGDQISSN DNLIFDDYRG KGCVDDSGFV 61 YKLGERFFPG HSNCPCVCAL DGPVCDQPEC PKIHPKCTKV EHNGCCPECK EVKNFCEYHG 121 KNYKILEEFK VCVTLHIY SEQ ID 40 (INSP 123 cloned mature nucleotide sequence 1)
• SEQ ID 41 (INSP 123 cloned mature polypeptide sequence 1) 1 AISHEDYPAD EGDQISSNDN LIFDDYRGKG CVDDSGFVYK LGERFFPGHS NCPCVCALDG 61 PVCDQPECPK IHPKCTKVEH NGCCPECKEV KNFCEYHGKN YKILEEFKVC VTLHIY
• SEQ ID 44 (INSP 123 cloned mature nucleotide sequence 3) 1 GATGAAGGTG ACCAGATCTC CAGTAATGAC AATCTGATCT TTGATGACTA TCGAGGGAAA
• SEQ ID 49 (INSP 124 cloned mature polypeptide sequence 1) 1 AISHEDYPAD EGDQISSNDN LIFDDYRGKG CVDDSGFVYK LGERFFPGHS NCPCVCALDG
• SEQ ID 51 (INSP 124 cloned mature polypeptide sequence 2) 1 AAISHEDYPA DEGDQISSND NLIFDDYRGK GCVDDSGFVY KLGERFFPGH SNCPCVCALD
• AAAATTCACC CAAAGTGTAC TAAAGTGGAA CACAATGGAT GCTGTCCTGA GTGCAAAGAA 241 GTAAAAAACT TCTGTGAATA TCACGGGAAA AATTACAAAA TCTTGGAGGA ATTTAAGCCC

Landscapes

• Health & Medical Sciences (AREA)
• Life Sciences & Earth Sciences (AREA)
• Chemical & Material Sciences (AREA)
• Organic Chemistry (AREA)
• Medicinal Chemistry (AREA)
• General Health & Medical Sciences (AREA)
• Veterinary Medicine (AREA)
• General Chemical & Material Sciences (AREA)
• Nuclear Medicine, Radiotherapy & Molecular Imaging (AREA)
• Chemical Kinetics & Catalysis (AREA)
• Pharmacology & Pharmacy (AREA)
• Animal Behavior & Ethology (AREA)
• Public Health (AREA)
• Bioinformatics & Cheminformatics (AREA)
• Engineering & Computer Science (AREA)
• Diabetes (AREA)
• Hematology (AREA)
• Physical Education & Sports Medicine (AREA)
• Oncology (AREA)
• Immunology (AREA)
• Orthopedic Medicine & Surgery (AREA)
• Rheumatology (AREA)
• Pulmonology (AREA)
• Neurology (AREA)
• Communicable Diseases (AREA)
• Neurosurgery (AREA)
• Biomedical Technology (AREA)
• Molecular Biology (AREA)
• Virology (AREA)
• Endocrinology (AREA)
• Heart & Thoracic Surgery (AREA)
• Obesity (AREA)
• Cardiology (AREA)
• Tropical Medicine & Parasitology (AREA)
• Proteomics, Peptides & Aminoacids (AREA)
• Genetics & Genomics (AREA)
• Urology & Nephrology (AREA)
• Biophysics (AREA)
• Biochemistry (AREA)
• Gastroenterology & Hepatology (AREA)

Applications Claiming Priority (2)

Publications (1)

Family

ID=9957338

Family Applications (1)

Country Status (13)

Families Citing this family (11)

Family Cites Families (1)

• 2003
  • 2003-04-30 GB GBGB0309916.5A patent/GB0309916D0/en not_active Ceased
• 2004
  • 2004-04-30 EP EP04730586A patent/EP1620466A2/en not_active Ceased
  • 2004-04-30 BR BRPI0409802-1A patent/BRPI0409802A/pt not_active IP Right Cessation
  • 2004-04-30 US US10/554,816 patent/US20070274992A1/en not_active Abandoned
  • 2004-04-30 EA EA200501711A patent/EA010405B1/ru not_active IP Right Cessation
  • 2004-04-30 MX MXPA05011424A patent/MXPA05011424A/es unknown
  • 2004-04-30 WO PCT/GB2004/001890 patent/WO2004096856A2/en active Application Filing
  • 2004-04-30 CA CA002522108A patent/CA2522108A1/en not_active Abandoned
  • 2004-04-30 KR KR1020057019715A patent/KR20060011957A/ko not_active Application Discontinuation
  • 2004-04-30 JP JP2006506210A patent/JP2007536892A/ja active Pending
  • 2004-04-30 CN CNA2004800184461A patent/CN1812998A/zh active Pending
  • 2004-04-30 AU AU2004234137A patent/AU2004234137A1/en not_active Abandoned
• 2005
  • 2005-11-30 NO NO20055669A patent/NO20055669L/no not_active Application Discontinuation

Non-Patent Citations (1)

Also Published As

Similar Documents

Legal Events